THERAPEUTIC USES OF GENOME EDITING WITH CRISPR/Cas SYSTEMS

ABSTRACT

Disclosed herein are methods, compositions, and kits for high efficiency, site-specific genomic editing of cells for treating or preventing genetic blood disorders.

RELATED APPLICATIONS

This application is a continuation of U.S. application Ser. No.14/509,924, filed Oct. 8, 2014, which is a continuation-in-part of PCTApplication No. PCT/US2014/46034, filed Jul. 9, 2014, which claims thebenefit of U.S. Provisional Application No. 61/844,333, filed on Jul. 9,2013, and 61/869,369, filed on Aug. 23, 2013. The entire teachings ofthe above applications are incorporated herein by reference.

GOVERNMENT SUPPORT

This invention was made with government support under HL118744,HL098364, DK095384 and HL107440 awarded by the National Institutes ofHealth. The government has certain rights in the invention.

BACKGROUND OF THE INVENTION

Clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated (Cas) systems are a new class ofgenome-editing tools that target desired genomic sites in mammaliancells. Recently published type II CRISPR/Cas systems use Cas9 nucleasethat is targeted to a genomic site by complexing with a synthetic guideRNA that hybridizes to a 20-nucleotide DNA sequence and immediatelypreceding an NGG motif recognized by Cas9 (thus, a (N)₂₀NGG target DNAsequence). This results in a double-strand break three nucleotidesupstream of the NGG motif. The double strand break instigates eithernon-homologous end-joining, which is error-prone and conducive toframeshift mutations that knock out gene alleles, or homology-directedrepair, which can be exploited with the use of an exogenously introduceddouble-strand or single-strand DNA repair template to knock in orcorrect a mutation in the genome. Thus, CRISPR/Cas systems could beuseful tools for therapeutic applications, but unfortunately priorpublished reports have demonstrated an efficiency of allele targeting ofonly 2%-4% in human stem cells (Mali et al., Science 339:823-826(2013)).

SUMMARY OF THE INVENTION

Work described herein demonstrates methods of allele targeting usingCRISPR/Cas systems resulting in mutant cells with efficiencies of up to80%. These vastly improved methods permit CRISPR/Cas systems to beutilized effectively for the first time for therapeutic purposes.Methods of delivery of CRISPR/Cas systems to human stem cells areprovided. In addition, methods of specifically identifying useful RNAguide sequences are provided, along with particular guide sequencesuseful in targeting specific genes (e.g., ADA, AK2, CD3D, DCLRE1C,IL2RG, IL7R, JAK3, LIG4, NHEJ1, PNP, PRKDC, RAG1, RAG2, ZAP70 and HBB).Moreover, methods of treatment (e.g., severe combined immunodeficiency,sickle cell disease, e.g., sickle cell anemia, beta thalassemia, etc.)utilizing the compositions and methods disclosed herein are provided. Insome aspects, disclosed herein is a method for altering a target severecombined immunodeficiency (SCID)-associated polynucleotide sequence in acell comprising contacting the SCID-associated polynucleotide sequencewith a clustered regularly interspaced short palindromicrepeats-associated (Cas) protein and from one to two ribonucleic acids,wherein the ribonucleic acids direct Cas protein to and hybridize to atarget motif of the target SCID-associated polynucleotide sequence,wherein the target SCID-associated polynucleotide sequence is cleaved.

In some aspects, disclosed herein is a method for treating or preventinga disorder associated with expression of a SCID-associatedpolynucleotide sequence in a subject, the method comprising (a) alteringa target SCID-associated polynucleotide sequence in a cell ex vivo bycontacting the SCID-associated polynucleotide sequence with a clusteredregularly interspaced short palindromic repeats-associated (Cas) proteinand from one to two ribonucleic acids, wherein the ribonucleic acidsdirect Cas protein to and hybridize to a target motif of the targetSCID-associated polynucleotide sequence, wherein the targetSCID-associated polynucleotide sequence is cleaved, and (b) introducingthe cell into the subject, thereby treating or preventing a disorderassociated with expression of the SCID-associated polynucleotidesequence.

In some aspects, disclosed herein is a method for treating or preventinga disorder associated with expression of a SCID-associatedpolynucleotide sequence in a subject, the method comprising altering atarget SCID-associated polynucleotide sequence in a cell by contactingthe SCID-associated polynucleotide sequence with a clustered regularlyinterspaced short palindromic repeats-associated (Cas) protein and fromone to two ribonucleic acids, wherein the ribonucleic acids direct Casprotein to and hybridize to a target motif of the target SCID-associatedpolynucleotide sequence, and wherein the target SCID-associatedpolynucleotide sequence is cleaved, thereby treating or preventing adisorder associated with expression of the SCID-associatedpolynucleotide sequence.

In some aspects, disclosed herein is a method for simultaneouslyaltering multiple target SCID-associated polynucleotide sequences in acell comprising contacting the SCID-associated polynucleotide sequenceswith a clustered regularly interspaced short palindromicrepeats-associated (Cas) protein and multiple ribonucleic acids, whereinthe ribonucleic acids direct Cas protein to and hybridize to targetmotifs of the target SCID-associated polynucleotide sequences, whereinthe target SCID-associated polynucleotide sequences are cleaved.

In some aspects, disclosed herein is a method for treating or preventinga disorder associated with expression of SCID-associated polynucleotidesequences in a subject, the method comprising (a) altering targetSCID-associated polynucleotide sequences in a cell ex vivo by contactingthe SCID-associated polynucleotide sequences with a clustered regularlyinterspaced short palindromic repeats-associated (Cas) protein andmultiple ribonucleic acids, wherein the ribonucleic acids direct Casprotein to and hybridize to target motifs of the target SCID-associatedpolynucleotide sequences, wherein the target SCID-associatedpolynucleotide sequences are cleaved, and (b) introducing the cell intothe subject, thereby treating or preventing a disorder associated withexpression of the SCID-associated polynucleotide sequences.

In some aspects, disclosed herein is a method for treating or preventinga disorder associated with expression of SCID-associated polynucleotidesequences in a subject, the method comprising altering targetSCID-associated polynucleotide sequences in a cell by contacting theSCID-associated polynucleotide sequences with a clustered regularlyinterspaced short palindromic repeats-associated (Cas) protein andmultiple ribonucleic acids, wherein the ribonucleic acids direct Casprotein to and hybridize to target moieties of the targetSCID-associated polynucleotide sequences, and wherein the targetSCID-associated polynucleotide sequences are cleaved, thereby treatingor preventing a disorder associated with expression of theSCID-associated polynucleotide sequences.

In some aspects, disclosed herein is a method for altering a targetsickle cell disease (SCD)-associated polynucleotide sequence in a cellcomprising contacting the SCD-associated polynucleotide sequence with aclustered regularly interspaced short palindromic repeats-associated(Cas) protein and from one to two ribonucleic acids, wherein theribonucleic acids direct Cas protein to and hybridize to a target motifof the target SCD-associated polynucleotide sequence, wherein the targetSCD-associated polynucleotide sequence is cleaved.

In some aspects, disclosed herein is a method for treating or preventinga disorder associated with expression of a SCD-associated polynucleotidesequence in a subject, the method comprising (a) altering a targetSCD-associated polynucleotide sequence in a cell ex vivo by contactingthe SCD-associated polynucleotide sequence with a clustered regularlyinterspaced short palindromic repeats-associated (Cas) protein and fromone to two ribonucleic acids, wherein the ribonucleic acids direct Casprotein to and hybridize to a target motif of the target SCD-associatedpolynucleotide sequence, wherein the target SCD-associatedpolynucleotide sequence is cleaved, and (b) introducing the cell intothe subject, thereby treating or preventing a disorder associated withexpression of the SCD-associated polynucleotide sequence.

In some aspects, disclosed herein is a method for treating or preventinga disorder associated with expression of a SCD-associated polynucleotidesequence in a subject, the method comprising altering a targetSCD-associated polynucleotide sequence in a cell by contacting theSCD-associated polynucleotide sequence with a clustered regularlyinterspaced short palindromic repeats-associated (Cas) protein and fromone to two ribonucleic acids, wherein the ribonucleic acids direct Casprotein to and hybridize to a target motif of the target SCD-associatedpolynucleotide sequence, and wherein the target SCD-associatedpolynucleotide sequence is cleaved, thereby treating or preventing adisorder associated with expression of the SCD-associated polynucleotidesequence.

In some aspects, disclosed herein is a method for simultaneouslyaltering multiple target SCD-associated polynucleotide sequences in acell comprising contacting the SCD-associated polynucleotide sequenceswith a clustered regularly interspaced short palindromicrepeats-associated (Cas) protein and multiple ribonucleic acids, whereinthe ribonucleic acids direct Cas protein to and hybridize to targetmotifs of the target SCD-associated polynucleotide sequences, whereinthe target SCD-associated polynucleotide sequences are cleaved.

In some aspects, disclosed herein is a method for treating or preventinga disorder associated with expression of SCD-associated polynucleotidesequences in a subject, the method comprising (a) altering targetSCD-associated polynucleotide sequences in a cell ex vivo by contactingthe SCD-associated polynucleotide sequences with a clustered regularlyinterspaced short palindromic repeats-associated (Cas) protein andmultiple ribonucleic acids, wherein the ribonucleic acids direct Casprotein to and hybridize to target motifs of the target SCD-associatedpolynucleotide sequences, wherein the target SCD-associatedpolynucleotide sequences are cleaved, and (b) introducing the cell intothe subject, thereby treating or preventing a disorder associated withexpression of the SCD-associated polynucleotide sequences.

In some aspects, disclosed herein is a method for treating or preventinga disorder associated with expression of SCD-associated polynucleotidesequences in a subject, the method comprising altering targetSCD-associated polynucleotide sequences in a cell by contacting theSCD-associated polynucleotide sequences with a clustered regularlyinterspaced short palindromic repeats-associated (Cas) protein andmultiple ribonucleic acids, wherein the ribonucleic acids direct Casprotein to and hybridize to target moieties of the target SCD-associatedpolynucleotide sequences, and wherein the target SCD-associatedpolynucleotide sequences are cleaved, thereby treating or preventing adisorder associated with expression of the SCD-associated polynucleotidesequences.

In some aspects, disclosed herein is a method for altering a target betathalassemia-associated polynucleotide sequence in a cell comprisingcontacting the beta thalassemia-associated polynucleotide sequence witha clustered regularly interspaced short palindromic repeats-associated(Cas) protein and from one to two ribonucleic acids, wherein theribonucleic acids direct Cas protein to and hybridize to a target motifof the target beta thalassemia-associated polynucleotide sequence,wherein the target beta thalassemia-associated polynucleotide sequenceis cleaved.

In some aspects, disclosed herein is a method for treating or preventinga disorder associated with expression of a beta thalassemia-associatedpolynucleotide sequence in a subject, the method comprising (a) alteringa target beta thalassemia-associated polynucleotide sequence in a cellex vivo by contacting the beta thalassemia-associated polynucleotidesequence with a clustered regularly interspaced short palindromicrepeats-associated (Cas) protein and from one to two ribonucleic acids,wherein the ribonucleic acids direct Cas protein to and hybridize to atarget motif of the target beta thalassemia-associated polynucleotidesequence, wherein the target beta thalassemia-associated polynucleotidesequence is cleaved, and (b) introducing the cell into the subject,thereby treating or preventing a disorder associated with expression ofthe beta thalassemia-associated polynucleotide sequence.

In some aspects, disclosed herein is a method for treating or preventinga disorder associated with expression of a beta thalassemia-associatedpolynucleotide sequence in a subject, the method comprising altering atarget beta thalassemia-associated polynucleotide sequence in a cell bycontacting the beta thalassemia-associated polynucleotide sequence witha clustered regularly interspaced short palindromic repeats-associated(Cas) protein and from one to two ribonucleic acids, wherein theribonucleic acids direct Cas protein to and hybridize to a target motifof the target beta thalassemia-associated polynucleotide sequence, andwherein the target beta thalassemia-associated polynucleotide sequenceis cleaved, thereby treating or preventing a disorder associated withexpression of the beta thalassemia-associated polynucleotide sequence.

In some aspects, disclosed herein is a method for simultaneouslyaltering multiple target beta thalassemia-associated polynucleotidesequences in a cell comprising contacting the betathalassemia-associated polynucleotide sequences with a clusteredregularly interspaced short palindromic repeats-associated (Cas) proteinand multiple ribonucleic acids, wherein the ribonucleic acids direct Casprotein to and hybridize to target motifs of the target betathalassemia-associated polynucleotide sequences, wherein the target betathalassemia-associated polynucleotide sequences are cleaved.

In some aspects, disclosed herein is a method for treating or preventinga disorder associated with expression of beta thalassemia-associatedpolynucleotide sequences in a subject, the method comprising (a)altering target beta thalassemia-associated polynucleotide sequences ina cell ex vivo by contacting the beta thalassemia-associatedpolynucleotide sequences with a clustered regularly interspaced shortpalindromic repeats-associated (Cas) protein and multiple ribonucleicacids, wherein the ribonucleic acids direct Cas protein to and hybridizeto target motifs of the target beta thalassemia-associatedpolynucleotide sequences, wherein the target beta thalassemia-associatedpolynucleotide sequences are cleaved, and (b) introducing the cell intothe subject, thereby treating or preventing a disorder associated withexpression of the beta thalassemia-associated polynucleotide sequences.

In some aspects, disclosed herein is a method for treating or preventinga disorder associated with expression of beta thalassemia-associatedpolynucleotide sequences in a subject, the method comprising alteringtarget beta thalassemia-associated polynucleotide sequences in a cell bycontacting the beta thalassemia-associated polynucleotide sequences witha clustered regularly interspaced short palindromic repeats-associated(Cas) protein and multiple ribonucleic acids, wherein the ribonucleicacids direct Cas protein to and hybridize to target moieties of thetarget beta thalassemia-associated polynucleotide sequences, and whereinthe target beta thalassemia-associated polynucleotide sequences arecleaved, thereby treating or preventing a disorder associated withexpression of the beta thalassemia-associated polynucleotide sequences.

In some embodiments, the Cas protein is Streptococcus pyogenes Cas9protein or a functional portion thereof. In some embodiments, thefunctional portion comprises a combination of operably linked Cas9protein functional domains selected from the group consisting of a DNAbinding domain, at least one RNA binding domain, a helicase domain, andan endonuclease domain. In some embodiments, the functional domains forma complex. In some embodiments, the Cas protein is Cas9 protein from anybacterial species or functional portion thereof. In some embodiments,the functional portion comprises a combination of operably linked Cas9protein functional domains selected from the group consisting of a DNAbinding domain, at least one RNA binding domain, a helicase domain, andan endonuclease domain. In some embodiments, the functional domains forma complex.

In some embodiments, the Cas protein is complexed with the one to tworibonucleic acids. In some embodiments, the Cas protein is complexedwith the multiple ribonucleic acids.

In some embodiments, the target motif is a 20-nucleotide DNA sequence.In some embodiments, each target motif is a 20-nucleotide DNA sequence.In some embodiments, the target motif is a 20-nucleotide DNA sequencebeginning with G and immediately precedes an NGG motif recognized by theCas protein. In some embodiments, each target motif is a 20-nucleotideDNA sequence beginning with G and immediately precedes an NGG motifrecognized by the Cas protein. In some embodiments, the target motif isa 20-nucleotide DNA sequence and immediately precedes an NGG motifrecognized by the Cas protein. In some embodiments, each target motif isa 20-nucleotide DNA sequence and immediately precedes an NGG motifrecognized by the Cas protein. In some embodiments, the target motif isG(N)₁₉NGG. In some embodiments, each target motif is G(N)₁₉NGG. In someembodiments, the target motif is (N)₂₀NGG. In some embodiments, eachtarget motif is (N)₂₀NGG.

In some embodiments, the target polynucleotide sequence is cleaved suchthat a double-strand break results. In some embodiments, each targetpolynucleotide sequence is cleaved such that a double-strand breakresults. In some embodiments, the target polynucleotide sequence iscleaved such that a single-strand break results. In some embodiments,each target polynucleotide sequence is cleaved such that a single-strandbreak results.

In some embodiments, the alteration is an indel. In some embodiments,the alteration results in reduced expression of the targetpolynucleotide sequence. In some embodiments, the alteration results inreduced expression of the target polynucleotide sequences. In someembodiments, the alteration results in a knock out of the targetpolynucleotide sequence. In some embodiments, the alteration results ina knock out of the target polynucleotide sequences. In some embodiments,the alteration results in correction of the target polynucleotidesequence from an undesired sequence to a desired sequence. In someembodiments, the alteration results in correction of the targetpolynucleotide sequences from undesired sequences to desired sequences.In some embodiments, the alteration is a homozygous alteration. In someembodiments, each alteration is a homozygous alteration.

In some embodiments, subsequent to cleavage of the target polynucleotidesequence, homology-directed repair occurs. In some embodiments,homology-directed repair is performed using an exogenously introducedDNA repair template. In some embodiments, the exogenously introduced DNArepair template is single-stranded. In some embodiments, the exogenouslyintroduced DNA repair template is double-stranded. In some embodiments,subsequent to cleavage of the target polynucleotide sequences,homology-directed repair occurs. In some embodiments, homology-directedrepair is performed using an exogenously introduced DNA repair template.In some embodiments, the exogenously introduced DNA repair template issingle-stranded. In some embodiments, the exogenously introduced DNArepair template is double-stranded.

In some embodiments, the cell is a peripheral blood cell. In someembodiments, the cell is a stem cell or a pluripotent cell. In someembodiments, the cell is a hematopoietic stem cell. In some embodiments,the cell is a CD34⁺ cell. In some embodiments, the cell is a CD34⁺mobilized peripheral blood cell. In some embodiments, the cell is aCD34⁺ cord blood cell. In some embodiments, the cell is a CD34⁺ bonemarrow cell. In some embodiments, the cell is aCD34⁺CD38-Lineage-CD90⁺CD45RA⁻cell.

In some embodiments, the target polynucleotide sequence is ADA. In someembodiments, at least one of the one to two ribonucleic acids comprisesa sequence selected from the group consisting of the ribonucleic acidsequences of FIG. 1 or at least a 12 nucleotide fragment thereof. Insome embodiments, at least one of the one to two ribonucleic acidscomprises a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of the ribonucleic acid sequences ofFIG. 1 or at least a 12 nucleotide fragment thereof.

In some embodiments, the target polynucleotide sequence is AK2. In someembodiments, at least one of the one to two ribonucleic acids comprisesa sequence selected from the group consisting of the ribonucleic acidsequences of FIG. 2 or at least a 12 nucleotide fragment thereof. Insome embodiments, at least one of the one to two ribonucleic acidscomprises a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of the ribonucleic acid sequences ofFIG. 2 or at least a 12 nucleotide fragment thereof.

In some embodiments, the target polynucleotide sequence is CD3D. In someembodiments, at least one of the one to two ribonucleic acids comprisesa sequence selected from the group consisting of the ribonucleic acidsequences of FIG. 3 or at least a 12 nucleotide fragment thereof. Insome embodiments, at least one of the one to two ribonucleic acidscomprises a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of the ribonucleic acid sequences ofFIG. 3 or at least a 12 nucleotide fragment thereof.

In some embodiments, the target polynucleotide sequence is DCLRE1C. Insome embodiments, at least one of the one to two ribonucleic acidscomprises a sequence selected from the group consisting of theribonucleic acid sequences of FIG. 4 or at least a 12 nucleotidefragment thereof. In some embodiments, at least one of the one to tworibonucleic acids comprises a sequence with a single nucleotide mismatchto a sequence selected from the group consisting of the ribonucleic acidsequences of FIG. 4 or at least a 12 nucleotide fragment thereof.

In some embodiments, the target polynucleotide sequence is IL2RG. Insome embodiments, at least one of the one to two ribonucleic acidscomprises a sequence selected from the group consisting of theribonucleic acid sequences of FIG. 6 or at least a 12 nucleotidefragment thereof. In some embodiments, at least one of the one to tworibonucleic acids comprises a sequence with a single nucleotide mismatchto a sequence selected from the group consisting of the ribonucleic acidsequences of FIG. 6 or at least a 12 nucleotide fragment thereof.

In some embodiments, the target polynucleotide sequence is IL7R. In someembodiments, at least one of the one to two ribonucleic acids comprisesa sequence selected from the group consisting of the ribonucleic acidsequences of FIG. 7 or at least a 12 nucleotide fragment thereof. Insome embodiments, at least one of the one to two ribonucleic acidscomprises a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of the ribonucleic acid sequences ofFIG. 7 or at least a 12 nucleotide fragment thereof.

In some embodiments, the target polynucleotide sequence is JAK3. In someembodiments, at least one of the one to two ribonucleic acids comprisesa sequence selected from the group consisting of the ribonucleic acidsequences of FIG. 8 or at least a 12 nucleotide fragment thereof. Insome embodiments, at least one of the one to two ribonucleic acidscomprises a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of the ribonucleic acid sequences ofFIG. 8 or at least a 12 nucleotide fragment thereof.

In some embodiments, the target polynucleotide sequence is LIG4. In someembodiments, at least one of the one to two ribonucleic acids comprisesa sequence selected from the group consisting of the ribonucleic acidsequences of FIG. 9 or at least a 12 nucleotide fragment thereof. Insome embodiments, at least one of the one to two ribonucleic acidscomprises a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of the ribonucleic acid sequences ofFIG. 9 or at least a 12 nucleotide fragment thereof.

In some embodiments, the target polynucleotide sequence is NHEJ1. Insome embodiments, at least one of the one to two ribonucleic acidscomprises a sequence selected from the group consisting of theribonucleic acid sequences of FIG. 10 or at least a 12 nucleotidefragment thereof. In some embodiments, at least one of the one to tworibonucleic acids comprises a sequence with a single nucleotide mismatchto a sequence selected from the group consisting of the ribonucleic acidsequences of FIG. 10 or at least a 12 nucleotide fragment thereof.

In some embodiments, the target polynucleotide sequence is PNP. In someembodiments, at least one of the one to two ribonucleic acids comprisesa sequence selected from the group consisting of the ribonucleic acidsequences of FIG. 11 or at least a 12 nucleotide fragment thereof. Insome embodiments, at least one of the one to two ribonucleic acidscomprises a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of the ribonucleic acid sequences ofFIG. 11 or at least a 12 nucleotide fragment thereof.

In some embodiments, the target polynucleotide sequence is PRKDC. Insome embodiments, at least one of the one to two ribonucleic acidscomprises a sequence selected from the group consisting of theribonucleic acid sequences of FIG. 12 or at least a 12 nucleotidefragment thereof. In some embodiments, at least one of the one to tworibonucleic acids comprises a sequence with a single nucleotide mismatchto a sequence selected from the group consisting of the ribonucleic acidsequences of FIG. 12 or at least a 12 nucleotide fragment thereof.

In some embodiments, the target polynucleotide sequence is RAG1. In someembodiments, at least one of the one to two ribonucleic acids comprisesa sequence selected from the group consisting of the ribonucleic acidsequences of FIG. 13 or at least a 12 nucleotide fragment thereof. Insome embodiments, at least one of the one to two ribonucleic acidscomprises a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of the ribonucleic acid sequences ofFIG. 13 or at least a 12 nucleotide fragment thereof.

In some embodiments, the target polynucleotide sequence is RAG2. In someembodiments, at least one of the one to two ribonucleic acids comprisesa sequence selected from the group consisting of the ribonucleic acidsequences of FIG. 14 or at least a 12 nucleotide fragment thereof. Insome embodiments, at least one of the one to two ribonucleic acidscomprises a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of the ribonucleic acid sequences ofFIG. 14 or at least a 12 nucleotide fragment thereof.

In some embodiments, the target polynucleotide sequence is ZAP70. Insome embodiments, at least one of the one to two ribonucleic acidscomprises a sequence selected from the group consisting of theribonucleic acid sequences of FIG. 15 or at least a 12 nucleotidefragment thereof. In some embodiments, at least one of the one to tworibonucleic acids comprises a sequence with a single nucleotide mismatchto a sequence selected from the group consisting of the ribonucleic acidsequences of FIG. 15 or at least a 12 nucleotide fragment thereof.

In some embodiments, the target polynucleotide sequence is HBB. In someembodiments, at least one of the one to two ribonucleic acids comprisesa sequence selected from the group consisting of the ribonucleic acidsequences of FIG. 5 or at least a 12 nucleotide fragment thereof. Insome embodiments, at least one of the one to two ribonucleic acidscomprises a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of the ribonucleic acid sequences ofFIG. 5 or at least a 12 nucleotide fragment thereof. In someembodiments, at least one of the one to two ribonucleic acids comprisesa sequence of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321) or at least a 12nucleotide fragment thereof. In some embodiments, at least one of theone to two ribonucleic acids comprises a sequence with a singlenucleotide mismatch to ribonucleic acid sequence GTAACGGCAGACTTCTCCACAGG(SEQ ID NO: 5321) or at least a 12 nucleotide fragment thereof.

In some embodiments, the target polynucleotide sequences comprisemultiple different portions of ADA. In some embodiments, each of themultiple ribonucleic acids comprises a different sequence selected fromthe group consisting of the ribonucleic acid sequences of FIG. 1 or atleast 12 nucleotide fragments thereof. In some embodiments, each of themultiple ribonucleic acids comprises a sequence with a single nucleotidemismatch to a different sequence selected from the group consisting ofthe ribonucleic acid sequences of FIG. 1 or at least 12 nucleotidefragments thereof.

In some embodiments, the target polynucleotide sequences comprisemultiple different portions of AK2. In some embodiments, each of themultiple ribonucleic acids comprises a different sequence selected fromthe group consisting of the ribonucleic acid sequences of FIG. 2 or atleast 12 nucleotide fragments thereof. In some embodiments, each of themultiple ribonucleic acids comprises a sequence with a single nucleotidemismatch to a different sequence selected from the group consisting ofthe ribonucleic acid sequences of FIG. 2 or at least 12 nucleotidefragments thereof.

In some embodiments, the target polynucleotide sequences comprisemultiple different portions of CD3D. In some embodiments, each of themultiple ribonucleic acids comprises a different sequence selected fromthe group consisting of the ribonucleic acid sequences of FIG. 3 or atleast 12 nucleotide fragments thereof. In some embodiments, each of themultiple ribonucleic acids comprises a sequence with a single nucleotidemismatch to a different sequence selected from the group consisting ofthe ribonucleic acid sequences of FIG. 3 or at least 12 nucleotidefragments thereof.

In some embodiments, the target polynucleotide sequences comprisemultiple different portions of DCLRE1C. In some embodiments, each of themultiple ribonucleic acids comprises a different sequence selected fromthe group consisting of the ribonucleic acid sequences of FIG. 4 or atleast 12 nucleotide fragments thereof. In some embodiments, each of themultiple ribonucleic acids comprises a sequence with a single nucleotidemismatch to a different sequence selected from the group consisting ofthe ribonucleic acid sequences of FIG. 4 or at least 12 nucleotidefragments thereof.

In some embodiments, the target polynucleotide sequences comprisemultiple different portions of IL2RG. In some embodiments, each of themultiple ribonucleic acids comprises a different sequence selected fromthe group consisting of the ribonucleic acid sequences of FIG. 6 or atleast 12 nucleotide fragments thereof. In some embodiments, each of themultiple ribonucleic acids comprises a sequence with a single nucleotidemismatch to a different sequence selected from the group consisting ofthe ribonucleic acid sequences of FIG. 6 or at least 12 nucleotidefragments thereof.

In some embodiments, the target polynucleotide sequences comprisemultiple different portions of IL7R. In some embodiments, each of themultiple ribonucleic acids comprises a different sequence selected fromthe group consisting of the ribonucleic acid sequences of FIG. 7 or atleast 12 nucleotide fragments thereof. In some embodiments, each of themultiple ribonucleic acids comprises a sequence with a single nucleotidemismatch to a different sequence selected from the group consisting ofthe ribonucleic acid sequences of FIG. 7 or at least 12 nucleotidefragments thereof.

In some embodiments, the target polynucleotide sequences comprisemultiple different portions of JAK3. In some embodiments, each of themultiple ribonucleic acids comprises a different sequence selected fromthe group consisting of the ribonucleic acid sequences of FIG. 8 or atleast 12 nucleotide fragments thereof. In some embodiments, each of themultiple ribonucleic acids comprises a sequence with a single nucleotidemismatch to a different sequence selected from the group consisting ofthe ribonucleic acid sequences of FIG. 8 or at least 12 nucleotidefragments thereof.

In some embodiments, the target polynucleotide sequences comprisemultiple different portions of LIG4. In some embodiments, each of themultiple ribonucleic acids comprises a different sequence selected fromthe group consisting of the ribonucleic acid sequences of FIG. 9 or atleast 12 nucleotide fragments thereof. In some embodiments, each of themultiple ribonucleic acids comprises a sequence with a single nucleotidemismatch to a different sequence selected from the group consisting ofthe ribonucleic acid sequences of FIG. 9 or at least 12 nucleotidefragments thereof.

In some embodiments, the target polynucleotide sequences comprisemultiple different portions of NHEJ1. In some embodiments, each of themultiple ribonucleic acids comprises a different sequence selected fromthe group consisting of the ribonucleic acid sequences of FIG. 10 or atleast 12 nucleotide fragments thereof. In some embodiments, each of themultiple ribonucleic acids comprises a sequence with a single nucleotidemismatch to a different sequence selected from the group consisting ofthe ribonucleic acid sequences of FIG. 10 or at least 12 nucleotidefragments thereof.

In some embodiments, the target polynucleotide sequences comprisemultiple different portions of PNP. In some embodiments, each of themultiple ribonucleic acids comprises a different sequence selected fromthe group consisting of the ribonucleic acid sequences of FIG. 11 or atleast 12 nucleotide fragments thereof. In some embodiments, each of themultiple ribonucleic acids comprises a sequence with a single nucleotidemismatch to a different sequence selected from the group consisting ofthe ribonucleic acid sequences of FIG. 11 or at least 12 nucleotidefragments thereof.

In some embodiments, the target polynucleotide sequences comprisemultiple different portions of PRKDC. In some embodiments, each of themultiple ribonucleic acids comprises a different sequence selected fromthe group consisting of the ribonucleic acid sequences of FIG. 12 or atleast 12 nucleotide fragments thereof. In some embodiments, each of themultiple ribonucleic acids comprises a sequence with a single nucleotidemismatch to a different sequence selected from the group consisting ofthe ribonucleic acid sequences of FIG. 12 or at least 12 nucleotidefragments thereof.

In some embodiments, the target polynucleotide sequences comprisemultiple different portions of RAG1. In some embodiments, each of themultiple ribonucleic acids comprises a different sequence selected fromthe group consisting of the ribonucleic acid sequences of FIG. 13 or atleast 12 nucleotide fragments thereof. In some embodiments, each of themultiple ribonucleic acids comprises a sequence with a single nucleotidemismatch to a different sequence selected from the group consisting ofthe ribonucleic acid sequences of FIG. 13 or at least 12 nucleotidefragments thereof.

In some embodiments, the target polynucleotide sequences comprisemultiple different portions of RAG2. In some embodiments, each of themultiple ribonucleic acids comprises a different sequence selected fromthe group consisting of the ribonucleic acid sequences of FIG. 14 or atleast 12 nucleotide fragments thereof. In some embodiments, each of themultiple ribonucleic acids comprises a sequence with a single nucleotidemismatch to a different sequence selected from the group consisting ofthe ribonucleic acid sequences of FIG. 14 or at least 12 nucleotidefragments thereof.

In some embodiments, the target polynucleotide sequences comprisemultiple different portions of ZAP70. In some embodiments, each of themultiple ribonucleic acids comprises a different sequence selected fromthe group consisting of the ribonucleic acid sequences of FIG. 15 or atleast 12 nucleotide fragments thereof. In some embodiments, each of themultiple ribonucleic acids comprises a sequence with a single nucleotidemismatch to a different sequence selected from the group consisting ofthe ribonucleic acid sequences of FIG. 15 or at least 12 nucleotidefragments thereof.

In some embodiments, the target polynucleotide sequences comprisemultiple different portions of HBB. In some embodiments, each of themultiple ribonucleic acids comprises a different sequence selected fromthe group consisting of the ribonucleic acid sequences of FIG. 5 or atleast 12 nucleotide fragments thereof. In some embodiments, each of themultiple ribonucleic acids comprises a sequence with a single nucleotidemismatch to a different sequence selected from the group consisting ofthe ribonucleic acid sequences of FIG. 5 or at least 12 nucleotidefragments thereof.

In some embodiments, the target polynucleotide sequences comprise atleast a portion of any combination of target polynucleotide sequencesselected from the group consisting of ADA, AK2, CD3D, DCLRE1C, IL2RG,IL7R, JAK3, LIG4, NHEJ1, PNP, PRKDC, RAG1, RAG2, and ZAP70. In someembodiments, each of the multiple ribonucleic acids comprises adifferent sequence selected from the group consisting of the ribonucleicacid sequences of FIGS. 1-15 or at least a 12 nucleotide fragmentthereof. In some embodiments, each of the multiple ribonucleic acidscomprises a sequence with a single nucleotide mismatch to a differentsequence selected from the group consisting of the ribonucleic acidsequences of FIGS. 1-15 or at least a 12 nucleotide fragment thereof.

In some embodiments, the disorder is SCID. In some embodiments, thedisorder is sickle cell disease. In some embodiments, the disorder isbeta thalassemia.

In some embodiments, the one to two ribonucleic acids are designed tohybridize to a target motif immediately adjacent to a deoxyribonucleicacid motif recognized by the Cas protein. In some embodiments, each ofthe one to two ribonucleic acids are designed to hybridize to targetmotifs immediately adjacent to deoxyribonucleic acid motifs recognizedby the Cas protein which flank a mutant allele located between thetarget motifs. In some embodiments, the multiple ribonucleic acids aredesigned to hybridize to target motifs immediately adjacent todeoxyribonucleic acid motifs recognized by the Cas protein. In someembodiments, the multiple ribonucleic acids are designed to hybridize totarget motifs immediately adjacent to deoxyribonucleic acid motifsrecognized by the Cas protein which flank mutant alleles located betweenthe target motifs. In some embodiments, the one to two ribonucleic acidsare selected to minimize hybridization with nucleic acid sequences otherthan the target polynucleotide sequence. In some embodiments, themultiple ribonucleic acids are selected to minimize hybridization withnucleic acid sequences other than the target polynucleotide sequence. Insome embodiments, the target motif is selected such that it contains atleast two mismatches when compared with all other genomic nucleotidesequences in the cell. In some embodiments, each target motif isselected such that it contains at least two mismatches when comparedwith all other genomic nucleotide sequences in the cell. In someembodiments, the target motif is selected such that it contains at leastone mismatch when compared with all other genomic nucleotide sequencesin the cell. In some embodiments, the target motif is selected such thatit contains at least one mismatch when compared with all other genomicnucleotide sequences in the cell. In some embodiments, the one to tworibonucleic acids hybridize to a target motif that it contains at leasttwo mismatches when compared with all other genomic nucleotide sequencesin the cell. In some embodiments, each of the multiple ribonucleic acidshybridize to target motifs that contain at least two mismatches whencompared with all other genomic nucleotide sequences in the cell. Insome embodiments, the one to two ribonucleic acids hybridize to a targetmotif that contains at least one mismatch when compared with all othergenomic nucleotide sequences in the cell. In some embodiments, each ofthe multiple ribonucleic acids hybridize to target motifs that containat least one mismatch when compared with all other genomic nucleotidesequences in the cell.

In some embodiments, the Cas protein and the one to two ribonucleicacids are contained in a nanoparticle. In some embodiments, the Casprotein and the one to two ribonucleic acids are contained in a lipidnanoparticle. In some embodiments, the lipid nanoparticle comprises atleast one of a cationic lipid, a neutral lipid, an amino lipid, asterol, and a PEG or PEG-modified lipid. In some embodiments, thecationic lipid is selected from the group consisting of ALNY-100,C12-200, DODAC, DDAB, DOTAP, DOTMA, DODMA, DLinDMA, DLenDMA, DLin-C-DAP,DLin-DAC, DLin-MA, DLinDAP, DLin-S-DMA, DLin-2-DMAP, DLin-TMA.C1,DLin-TAP.C1, DLin-MPZ, DLinAP, DOAP, DLin-EG-DMA, DLinDMA, DLin-K-DMA,DLin-KC2-DMA, DLin-M-C3-DMA, KC2, MC3, DOTAP.C1, DOSPA, DOGS, DOPE,DODAP, DMRIE, XTC, and mixtures thereof. In some embodiments, theneutral lipid is selected from the group consisting of DPSC, DPPC, POPC,DOPE, SM, and mixtures thereof. In some embodiments, the PEG-modifiedlipid is selected from the group consisting of PEG-DMG, PEG-CerC14,PEG-CerC20, and mixtures thereof. In some embodiments, the Cas proteinand the multiple ribonucleic acids are contained in nanoparticles. Insome embodiments, the Cas protein and the multiple ribonucleic acids arecontained in lipid nanoparticles. In some embodiments, the lipidnanoparticles comprise at least one of a cationic lipid, a neutrallipid, an amino lipid, a sterol, and a PEG or PEG-modified lipid. Insome embodiments, the cationic lipid is selected from the groupconsisting of ALNY-100, C12-200, DODAC, DDAB, DOTAP, DOTMA, DODMA,DLinDMA, DLenDMA, DLin-C-DAP, DLin-DAC, DLin-MA, DLinDAP, DLin-S-DMA,DLin-2-DMAP, DLin-TMA.C1, DLin-TAP.C1, DLin-MPZ, DLinAP, DOAP,DLin-EG-DMA, DLinDMA, DLin-K-DMA, DLin-KC2-DMA, DLin-M-C3-DMA, KC2, MC3,DOTAP.C1, DOSPA, DOGS, DOPE, DODAP, DMRIE, XTC, and mixtures thereof. Insome embodiments, the neutral lipid is selected from the groupconsisting of DPSC, DPPC, POPC, DOPE, SM, and mixtures thereof. In someembodiments, the PEG-modified lipid is selected from the groupconsisting of PEG-DMG, PEG-CerC14, PEG-CerC20, and mixtures thereof.

In some embodiments, the efficiency of alteration at each loci is fromabout 50% to about 80%. In some embodiments, the efficiency ofalteration is at least about 5%. In some embodiments, the efficiency ofalteration is at least about 10%. In some embodiments, the efficiency ofalteration is from about 50% to about 80%.

In some embodiments, the Cas protein is encoded by a modified nucleicacid. In some embodiments, the modified nucleic acid comprises aribonucleic acid containing at least one modified nucleotide selectedfrom the group consisting of pseudouridine, 5-methylcytodine,2-thio-uridine, 5-methyluridine-5′-triphosphate,4-thiouridine-5′-triphosphate, 5,6-dihydrouridine-5′-triphosphate, and5-azauridine-5′-triphosphate. In some embodiments, at least one of theribonucleic acids is a modified ribonucleic acid comprising one to twomodified nucleotides selected from the group consisting ofpseudouridine, 5-methylcytodine, 2-thio-uridine,5-methyluridine-5′-triphosphate, 4-thiouridine-5′-triphosphate,5,6-dihydrouridine-5′-triphosphate, and 5-azauridine-5′-triphosphate.

In some embodiments, any of the Cas protein or the ribonucleic acids areexpressed from a plasmid. In some embodiments, any of the Cas protein orthe ribonucleic acids are expressed using a promoter optimized forincreased expression in stem cells. In some embodiments, the promoter isselected from the group consisting of a Cytomegalovirus (CMV) earlyenhancer element and a chicken beta-actin promoter, a chicken beta-actinpromoter, an elongation factor-1 alpha promoter, and a ubiquitinpromoter.

In some embodiments, the method further comprises selecting cells thatexpress the Cas protein. In some embodiments, selecting cells comprisesFACS. In some embodiments, FACs is used to select cells which co-expressCas and a fluorescent protein selected from the group consisting ofgreen fluorescent protein and red fluorescent protein.

In some aspects, disclosed herein is a method for altering a targetSCID-associated polynucleotide sequence in a cell comprising contactingthe SCID-associated polynucleotide sequence in a cell selected from thegroup consisting of a human pluripotent cell, a primary human cell, anda non-transformed human cell, with a clustered regularly interspacedshort palindromic repeats-associated (Cas) protein and from one to tworibonucleic acids, wherein the ribonucleic acids direct Cas protein toand hybridize to a target motif of the target SCID-associatedpolynucleotide sequence, wherein the target SCID-associatedpolynucleotide sequence is cleaved, and wherein the efficiency ofalteration of cells that express Cas protein is from about 8% to about80%.

In some aspects, disclosed herein is a method for altering a targetSCD-associated polynucleotide sequence in a cell comprising contactingthe SCD-associated polynucleotide sequence in a cell selected from thegroup consisting of a human pluripotent cell, a primary human cell, anda non-transformed human cell, with a clustered regularly interspacedshort palindromic repeats-associated (Cas) protein and from one to tworibonucleic acids, wherein the ribonucleic acids direct Cas protein toand hybridize to a target motif of the target SCD-associatedpolynucleotide sequence, wherein the target SCD-associatedpolynucleotide sequence is cleaved, and wherein the efficiency ofalteration of cells that express Cas protein is from about 8% to about80%.

In some aspects, disclosed herein is a method for altering a target betathalassemia-associated polynucleotide sequence in a cell comprisingcontacting the beta thalassemia-associated polynucleotide sequence in acell selected from the group consisting of a human pluripotent cell, aprimary human cell, and a non-transformed human cell, with a clusteredregularly interspaced short palindromic repeats-associated (Cas) proteinand from one to two ribonucleic acids, wherein the ribonucleic acidsdirect Cas protein to and hybridize to a target motif of the target betathalassemia-associated polynucleotide sequence, wherein the target betathalassemia-associated polynucleotide sequence is cleaved, and whereinthe efficiency of alteration of cells that express Cas protein is fromabout 8% to about 80%.

In some aspects, disclosed herein is a method for treating or preventinga disorder associated with expression of a SCID-associatedpolynucleotide sequence in a subject, the method comprising (a) alteringa target SCID-associated polynucleotide sequence in a cell ex vivo bycontacting the SCID-associated polynucleotide sequence in a cellselected from the group consisting of a human pluripotent cell, aprimary human cell, and a non-transformed human cell, with a clusteredregularly interspaced short palindromic repeats-associated (Cas) proteinand from one to two ribonucleic acids, wherein the ribonucleic acidsdirect Cas protein to and hybridize to a target motif of the targetSCID-associated polynucleotide sequence, wherein the targetSCID-associated polynucleotide sequence is cleaved, and wherein theefficiency of alteration is from about 8% to about 80%, and (b)introducing the cell into the subject, thereby treating or preventing adisorder associated with expression of the SCID-associatedpolynucleotide sequence.

In some aspects, disclosed herein is a method for treating or preventinga disorder associated with expression of a SCD-associated polynucleotidesequence in a subject, the method comprising (a) altering a targetSCD-associated polynucleotide sequence in a cell ex vivo by contactingthe SCD-associated polynucleotide sequence in a cell selected from thegroup consisting of a human pluripotent cell, a primary human cell, anda non-transformed human cell, with a clustered regularly interspacedshort palindromic repeats-associated (Cas) protein and from one to tworibonucleic acids, wherein the ribonucleic acids direct Cas protein toand hybridize to a target motif of the target SCD-associatedpolynucleotide sequence, wherein the target SCD-associatedpolynucleotide sequence is cleaved, and wherein the efficiency ofalteration is from about 8% to about 80%, and (b) introducing the cellinto the subject, thereby treating or preventing a disorder associatedwith expression of the SCD-associated polynucleotide sequence.

In some aspects, disclosed herein is a method for treating or preventinga disorder associated with expression of a beta thalassemia-associatedpolynucleotide sequence in a subject, the method comprising (a) alteringa target beta thalassemia-associated polynucleotide sequence in a cellex vivo by contacting the beta thalassemia-associated polynucleotidesequence in a cell selected from the group consisting of a humanpluripotent cell, a primary human cell, and a non-transformed humancell, with a clustered regularly interspaced short palindromicrepeats-associated (Cas) protein and from one to two ribonucleic acids,wherein the ribonucleic acids direct Cas protein to and hybridize to atarget motif of the target beta thalassemia-associated polynucleotidesequence, wherein the target beta thalassemia-associated polynucleotidesequence is cleaved, and wherein the efficiency of alteration is fromabout 8% to about 80%, and (b) introducing the cell into the subject,thereby treating or preventing a disorder associated with expression ofthe beta thalassemia-associated polynucleotide sequence.

In some aspects, disclosed herein is a method for simultaneouslyaltering multiple target SCID-associated polynucleotide sequences in acell comprising contacting the SCID-associated polynucleotide sequencesin a cell selected from the group consisting of a human pluripotentcell, a primary human cell, and a non-transformed human cell, with aclustered regularly interspaced short palindromic repeats-associated(Cas) protein and multiple ribonucleic acids, wherein the ribonucleicacids direct Cas protein to and hybridize to target motifs of the targetSCID-associated polynucleotide sequences, wherein the targetSCID-associated polynucleotide sequences are cleaved, and wherein theefficiency of alteration of cells that express Cas protein is from about8% to about 80%.

In some aspects, disclosed herein is a method for simultaneouslyaltering multiple target SCD-associated polynucleotide sequences in acell comprising contacting the SCD-associated polynucleotide sequencesin a cell selected from the group consisting of a human pluripotentcell, a primary human cell, and a non-transformed human cell, with aclustered regularly interspaced short palindromic repeats-associated(Cas) protein and multiple ribonucleic acids, wherein the ribonucleicacids direct Cas protein to and hybridize to target motifs of the targetSCD-associated polynucleotide sequences, wherein the targetSCD-associated polynucleotide sequences are cleaved, and wherein theefficiency of alteration of cells that express Cas protein is from about8% to about 80%.

In some aspects, disclosed herein is a method for simultaneouslyaltering multiple target beta thalassemia-associated polynucleotidesequences in a cell comprising contacting the betathalassemia-associated polynucleotide sequences in a cell selected fromthe group consisting of a human pluripotent cell, a primary human cell,and a non-transformed human cell, with a clustered regularly interspacedshort palindromic repeats-associated (Cas) protein and multipleribonucleic acids, wherein the ribonucleic acids direct Cas protein toand hybridize to target motifs of the target beta thalassemia-associatedpolynucleotide sequences, wherein the target beta thalassemia-associatedpolynucleotide sequences are cleaved, and wherein the efficiency ofalteration of cells that express Cas protein is from about 8% to about80%.

In some aspects, disclosed herein is a method for treating or preventinga disorder associated with expression of SCID-associated polynucleotidesequences in a subject, the method comprising (a) altering targetSCID-associated polynucleotide sequences in a cell ex vivo by contactingthe SCID-associated polynucleotide sequences in a cell selected from thegroup consisting of a human pluripotent cell, a primary human cell, anda non-transformed human cell, with a clustered regularly interspacedshort palindromic repeats-associated (Cas) protein and multipleribonucleic acids, wherein the ribonucleic acids direct Cas protein toand hybridize to target motifs of the target SCID-associatedpolynucleotide sequences, wherein the target SCID-associatedpolynucleotide sequences are cleaved, and wherein the efficiency ofalteration of cells that express Cas protein is from about 8% to about80%, and (b) introducing the cell into the subject, thereby treating orpreventing a disorder associated with expression of the SCID-associatedpolynucleotide sequences.

In some aspects, disclosed herein is a method for treating or preventinga disorder associated with expression of SCD-associated polynucleotidesequences in a subject, the method comprising (a) altering targetSCD-associated polynucleotide sequences in a cell ex vivo by contactingthe SCD-associated polynucleotide sequences in a cell selected from thegroup consisting of a human pluripotent cell, a primary human cell, anda non-transformed human cell, with a clustered regularly interspacedshort palindromic repeats-associated (Cas) protein and multipleribonucleic acids, wherein the ribonucleic acids direct Cas protein toand hybridize to target motifs of the target SCD-associatedpolynucleotide sequences, wherein the target SCD-associatedpolynucleotide sequences are cleaved, and wherein the efficiency ofalteration of cells that express Cas protein is from about 8% to about80%, and (b) introducing the cell into the subject, thereby treating orpreventing a disorder associated with expression of the SCD-associatedpolynucleotide sequences.

In some aspects, disclosed herein is a method for treating or preventinga disorder associated with expression of beta thalassemia-associatedpolynucleotide sequences in a subject, the method comprising (a)altering target beta thalassemia-associated polynucleotide sequences ina cell ex vivo by contacting the beta thalassemia-associatedpolynucleotide sequences in a cell selected from the group consisting ofa human pluripotent cell, a primary human cell, and a non-transformedhuman cell, with a clustered regularly interspaced short palindromicrepeats-associated (Cas) protein and multiple ribonucleic acids, whereinthe ribonucleic acids direct Cas protein to and hybridize to targetmotifs of the target SCID-associated polynucleotide sequences, whereinthe target beta thalassemia-associated polynucleotide sequences arecleaved, and wherein the efficiency of alteration of cells that expressCas protein is from about 8% to about 80%, and (b) introducing the cellinto the subject, thereby treating or preventing a disorder associatedwith expression of the beta thalassemia-associated polynucleotidesequences.

In some aspects, disclosed herein is a composition, comprising at leastone ribonucleic acid having a sequence selected from the groupconsisting of the ribonucleic acid sequences of FIGS. 1-15 or at least a12 nucleotide fragment thereof.

In some aspects, disclosed herein is a composition, comprising at leastone ribonucleic acid comprising a sequence with a single nucleotidemismatch to a sequence selected from the group consisting of theribonucleic acid sequences of FIGS. 1-15 or at least a 12 nucleotidefragment thereof.

In some embodiments, the at least one ribonucleic acid is contained in ananoparticle. In some embodiments, the at least one ribonucleic acid iscontained in a lipid nanoparticle. In some embodiments, the lipidnanoparticle comprises at least one of a cationic lipid, a neutrallipid, an amino lipid, a sterol, and a PEG or PEG-modified lipid. Insome embodiments, the cationic lipid is selected from the groupconsisting of ALNY-100, C12-200, DODAC, DDAB, DOTAP, DOTMA, DODMA,DLinDMA, DLenDMA, DLin-C-DAP, DLin-DAC, DLin-MA, DLinDAP, DLin-S-DMA,DLin-2-DMAP, DLin-TMA.C1, DLin-TAP.C1, DLin-MPZ, DLinAP, DOAP,DLin-EG-DMA, DLinDMA, DLin-K-DMA, DLin-KC2-DMA, DLin-M-C3-DMA, KC2, MC3,DOTAP.C1, DOSPA, DOGS, DOPE, DODAP, DMRIE, XTC, and mixtures thereof. Insome embodiments, the neutral lipid is selected from the groupconsisting of DPSC, DPPC, POPC, DOPE, SM, and mixtures thereof. In someembodiments, the PEG-modified lipid is selected from the groupconsisting of PEG-DMG, PEG-CerC14, PEG-CerC20, and mixtures thereof. Insome embodiments, at least one of the ribonucleic acids is a modifiedribonucleic acid comprising one to two modified nucleotides selectedfrom the group consisting of pseudouridine, 5-methylcytodine,2-thio-uridine, 5-methyluridine-5′-triphosphate,4-thiouridine-5′-triphosphate, 5,6-dihydrouridine-5′-triphosphate, and5-azauridine-5′-triphosphate.

In some embodiments, a composition further comprises a nucleic acidsequence encoding a Cas protein.

In some embodiments, a composition further comprises a nucleic acidsequence encoding a Cas9 protein or a functional portion thereof. Insome embodiments, the nucleic acid comprises a modified ribonucleic acidcomprising at least one modified nucleotide selected from the groupconsisting of pseudouridine, 5-methylcytodine, 2-thio-uridine,5-methyluridine-5′-triphosphate, 4-thiouridine-5′-triphosphate,5,6-dihydrouridine-5′-triphosphate, and 5-azauridine-5′-triphosphate.

In some aspects, disclosed herein is a composition, comprising achimeric nucleic acid comprising a ribonucleic acid encoding a Casprotein and at least one additional ribonucleic acid having a sequenceselected from the group consisting of the ribonucleic acid sequences ofFIGS. 1-15 or at least a 12 nucleotide fragment thereof.

In some aspects, disclosed herein is a composition, n comprising achimeric nucleic acid comprising a ribonucleic acid encoding a Casprotein and at least one additional ribonucleic acid sequence comprisinga sequence with a single nucleotide mismatch to a sequence selected fromthe group consisting of the ribonucleic acid sequences of FIGS. 1-15 orat least a 12 nucleotide fragment thereof.

In some embodiments, the composition further comprises a nucleic acidsequence encoding a fluorescent protein selected from the groupconsisting of green fluorescent protein and red fluorescent protein. Insome embodiments, the composition further comprises a promoter operablylinked to the chimeric nucleic acid. In some embodiments, the promoteris optimized for increased expression in human stem cells. In someembodiments, the promoter is selected from the group consisting of aCytomegalovirus (CMV) early enhancer element and a chicken beta-actinpromoter, a chicken beta-actin promoter, an elongation factor-1 alphapromoter, and a ubiquitin promoter.

In some embodiments, the chimeric nucleic acid is contained in ananoparticle. In some embodiments, the chimeric nucleic acid iscontained in a lipid nanoparticle. In some embodiments, the lipidnanoparticle comprises at least one of a cationic lipid, a neutrallipid, an amino lipid, a sterol, and a PEG or PEG-modified lipid. Insome embodiments, the cationic lipid is selected from the groupconsisting of ALNY-100, C12-200, DODAC, DDAB, DOTAP, DOTMA, DODMA,DLinDMA, DLenDMA, DLin-C-DAP, DLin-DAC, DLin-MA, DLinDAP, DLin-S-DMA,DLin-2-DMAP, DLin-TMA.C1, DLin-TAP.C1, DLin-MPZ, DLinAP, DOAP,DLin-EG-DMA, DLinDMA, DLin-K-DMA, DLin-KC2-DMA, DLin-M-C3-DMA, KC2, MC3,DOTAP.C1, DOSPA, DOGS, DOPE, DODAP, DMRIE, XTC, and mixtures thereof. Insome embodiments, the neutral lipid is selected from the groupconsisting of DPSC, DPPC, POPC, DOPE, SM, and mixtures thereof. In someembodiments, the PEG-modified lipid is selected from the groupconsisting of PEG-DMG, PEG-CerC14, PEG-CerC20, and mixtures thereof. Insome embodiments, the chimeric nucleic acid comprises at least onemodified nucleotide selected from the group consisting of pseudouridine,5-methylcytodine, 2-thio-uridine, 5-methyluridine-5′-triphosphate,4-thiouridine-5′-triphosphate, 5,6-dihydrouridine-5′-triphosphate, and5-azauridine-5′-triphosphate.

In some embodiments, the Cas protein comprises a Cas9 protein or afunctional portion thereof.

In some aspects, disclosed herein is a kit for altering a targetpolynucleotide sequence in a cell comprising a Cas9 protein or a nucleicacid encoding the Cas9 protein, and at least one ribonucleic acidsequence selected from the group consisting of the ribonucleic acidsequences of FIGS. 1-15, a sequence with a single nucleotide mismatch toa ribonucleic acid sequence of FIGS. 1-15 or at least a 12 nucleotidefragment thereof.

In some embodiments, the kit further comprises one or more cell lines,cultures, or populations selected from the group consisting of humanpluripotent cells, primary human cells, and non-transformed cells. Insome embodiments, the kit further comprises a DNA repair templateselected from the group consisting of an ADA DNA repair template, a AK2DNA repair template, a CD3D DNA repair template, a DCLRE1C DNA repairtemplate, a IL2RG DNA repair template, IL7R DNA repair template, a JAK3DNA repair template, a LIG4 DNA repair template, a NHEJ1 DNA repairtemplate, a PNP DNA repair template, a PRKDC DNA repair template, a RAG1DNA repair template, a RAG2 DNA repair template, a ZAP70 DNA repairtemplate, and a HBB DNA repair template.

In some aspects, the disclosure provides a composition comprising atleast one ribonucleic acid having a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321) or at least a 12 nucleotidefragment thereof. In some aspects, the disclosure provides a compositioncomprising at least one ribonucleic acid comprising a sequence with asingle nucleotide mismatch to a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321) or at least a 12 nucleotidefragment thereof. In some embodiments, the at least one ribonucleic acidis contained in a nanoparticle. In some embodiments, the at least oneribonucleic acid is contained in a lipid nanoparticle. In someembodiments, the lipid nanoparticle comprises at least one of a cationiclipid, a neutral lipid, an amino lipid, a sterol, and a PEG orPEG-modified lipid. In some embodiments, the cationic lipid is selectedfrom the group consisting of ALNY-100, C12-200, DODAC, DDAB, DOTAP,DOTMA, DODMA, DLinDMA, DLenDMA, DLin-C-DAP, DLin-DAC, DLin-MA, DLinDAP,DLin-S-DMA, DLin-2-DMAP, DLin-TMA.C1, DLin-TAP.C1, DLin-MPZ, DLinAP,DOAP, DLin-EG-DMA, DLinDMA, DLin-K-DMA, DLin-KC2-DMA, DLin-M-C3-DMA,KC2, MC3, DOTAP.C1, DOSPA, DOGS, DOPE, DODAP, DMRIE, XTC, and mixturesthereof. In some embodiments, the neutral lipid is selected from thegroup consisting of DPSC, DPPC, POPC, DOPE, SM, and mixtures thereof. Insome embodiments, the PEG-modified lipid is selected from the groupconsisting of PEG-DMG, PEG-CerC14, PEG-CerC20, and mixtures thereof. Insome embodiments, at least one of the ribonucleic acids is a modifiedribonucleic acid comprising one to two modified nucleotides selectedfrom the group consisting of pseudouridine, 5-methylcytodine,2-thio-uridine, 5-methyluridine-5′-triphosphate,4-thiouridine-5′-triphosphate, 5,6-dihydrouridine-5′-triphosphate, and5-azauridine-5′-triphosphate. In some embodiments, the compositionincludes a nucleic acid sequence encoding a Cas protein. In someembodiments, the composition includes a nucleic acid sequence encoding aCas9 protein or a functional portion thereof. In some embodiments, thenucleic acid comprises a modified ribonucleic acid comprising at leastone modified nucleotide selected from the group consisting ofpseudouridine, 5-methylcytodine, 2-thio-uridine,5-methyluridine-5′-triphosphate, 4-thiouridine-5′-triphosphate,5,6-dihydrouridine-5′-triphosphate, and 5-azauridine-5′-triphosphate.

In some aspects, the disclosure provides a composition comprising achimeric nucleic acid comprising a ribonucleic acid encoding a Casprotein and at least one additional ribonucleic acid having aribonucleic acid sequences of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321)or at least a 12 nucleotide fragment thereof. In some aspects, thedisclosure provides a composition comprising a chimeric nucleic acidcomprising a ribonucleic acid encoding a Cas protein and at least oneadditional ribonucleic acid sequence comprising a sequence with a singlenucleotide mismatch to a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321) or at least a 12 nucleotidefragment thereof. In some embodiments, the composition includes anucleic acid sequence encoding a fluorescent protein selected from thegroup consisting of green fluorescent protein and red fluorescentprotein. In some embodiments, the composition includes a promoteroperably linked to the chimeric nucleic acid. In some embodiments, thepromoter is optimized for increased expression in human stem cells. Insome embodiments, the promoter is selected from the group consisting ofa Cytomegalovirus (CMV) early enhancer element and a chicken beta-actinpromoter, a chicken beta-actin promoter, an elongation factor-1 alphapromoter, and a ubiquitin promoter. In some embodiments, the chimericnucleic acid is contained in a nanoparticle. In some embodiments, thechimeric nucleic acid is contained in a lipid nanoparticle. In someembodiments, the lipid nanoparticle comprises at least one of a cationiclipid, a neutral lipid, an amino lipid, a sterol, and a PEG orPEG-modified lipid. In some embodiments, the cationic lipid is selectedfrom the group consisting of ALNY-100, C12-200, DODAC, DDAB, DOTAP,DOTMA, DODMA, DLinDMA, DLenDMA, DLin-C-DAP, DLin-DAC, DLin-MA, DLinDAP,DLin-S-DMA, DLin-2-DMAP, DLin-TMA.C1, DLin-TAP.C1, DLin-MPZ, DLinAP,DOAP, DLin-EG-DMA, DLinDMA, DLin-K-DMA, DLin-KC2-DMA, DLin-M-C3-DMA,KC2, MC3, DOTAP.C1, DOSPA, DOGS, DOPE, DODAP, DMRIE, XTC, and mixturesthereof. In some embodiments, the neutral lipid is selected from thegroup consisting of DPSC, DPPC, POPC, DOPE, SM, and mixtures thereof. Insome embodiments, the PEG-modified lipid is selected from the groupconsisting of PEG-DMG, PEG-CerC14, PEG-CerC20, and mixtures thereof. Insome embodiments, the chimeric nucleic acid comprises at least onemodified nucleotide selected from the group consisting of pseudouridine,5-methylcytodine, 2-thio-uridine, 5-methyluridine-5′-triphosphate,4-thiouridine-5′-triphosphate, 5,6-dihydrouridine-5′-triphosphate, and5-azauridine-5′-triphosphate. In some embodiments, the Cas proteincomprises a Cas9 protein or a functional portion thereof.

In some aspects, the disclosure provides a kit for altering a targetpolynucleotide sequence in a cell comprising a Cas9 protein or a nucleicacid encoding the Cas9 protein, and at least one ribonucleic acidsequence selected from the group consisting of the ribonucleic acidsequences of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321), a sequence witha single nucleotide mismatch to a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321) or at least a 12 nucleotidefragment thereof. In some embodiments, the kit includes one or more celllines, cultures, or populations selected from the group consisting ofhuman pluripotent cells, primary human cells, and non-transformed cells.In some embodiments, the kit includes a HBB DNA repair template.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 shows exemplary guide RNA sequences useful when the targetpolynucleotide sequence is human ADA.

FIG. 2 shows exemplary guide RNA sequences useful when the targetpolynucleotide sequence is human AK2.

FIG. 3 shows exemplary guide RNA sequences useful when the targetpolynucleotide sequence is human CD3D.

FIG. 4 shows exemplary guide RNA sequences useful when the targetpolynucleotide sequence is human DCLRE1C.

FIG. 5 shows exemplary guide RNA sequences useful when the targetpolynucleotide sequence is human HBB.

FIG. 6 shows exemplary guide RNA sequences useful when the targetpolynucleotide sequence is human IL2RG.

FIG. 7 shows exemplary guide RNA sequences useful when the targetpolynucleotide sequence is human IL7R.

FIG. 8 shows exemplary guide RNA sequences useful when the targetpolynucleotide sequence is human JAK3.

FIG. 9 shows exemplary guide RNA sequences useful when the targetpolynucleotide sequence is human LIG4.

FIG. 10 shows exemplary guide RNA sequences useful when the targetpolynucleotide sequence is human NHEJ1.

FIG. 11 shows exemplary guide RNA sequences useful when the targetpolynucleotide sequence is human PNP.

FIG. 12 shows exemplary guide RNA sequences useful when the targetpolynucleotide sequence is human PRKDC.

FIG. 13 shows exemplary guide RNA sequences useful when the targetpolynucleotide sequence is human RAG1.

FIG. 14 shows exemplary guide RNA sequences useful when the targetpolynucleotide sequence is human RAG2.

FIG. 15 shows exemplary guide RNA sequences useful when the targetpolynucleotide sequence is human ZAP70.

FIG. 16 shows an exemplary amino acid sequence of a Cas protein. Yellowhighlights indicate Ruv-C-like domain. Underlining indicates HNHnuclease domain.

FIGS. 17A, 17B, 17C and 17D demonstrate targeted capture and extremelydeep sequencing of on-target and predicted off-target sites in CD34+HPSCs. FIG. 17A is a schematic overview of targeted capture and deepsequencing of on-target and predicted off-target sites (red bar). A 500bp flanking cutting site (in yellow) were included in sequence analysisfor detection of structural rearrangements, including translocations.Probe sets are indicated in blue. FIG. 17B features plots showingconsistent sequencing depth coverage at both on-target (left panel) andoff-target (right panel) sites, achieving a coverage exceeding 3,000×for all on-target sites. Decrease in sequencing depth at the on-targetsites in dual-gRNA libraries is marked by arrow, supporting predicteddeletions (bottom left; i=35 bp, ii=205 bp, iii=205 bp). FIG. 17C is aTable depicting the precise estimation of on-target mutation allelefrequencies by capture sequencing. Notably, the observed rate ofeffective null mutation exceeds previous estimates by PCR validation ofpredictable deletions, as smaller InDels and inversions also occur atappreciable frequencies. FIG. 17D is a Table depicting the estimation ofmutation frequencies at predicted off-target sites (*One off-target sitewas statistically different from controls following correction formultiple comparisons; p≤7.6×10⁻¹¹). N-fold enrichment is determinedbased on the ratio of non-reference reads in treated libraries comparedto untreated library. Each value represents the average of alloff-target sites for a given single gRNA or dual-gRNA experiment.Enrichment of 1 is equivalent to baseline (untreated control). **Forreference to on-target enrichments, on-target combined represents theproportion of non-reference reads (including single and dual-gRNAtreatments using a given gRNA) to total reads at on-target sites intreatment compared to control.

FIGS. 18A and 18B demonstrate potential off-target sites identified inCCR5 homologue CCR2 and analysis of events detected at the singleoff-target site in which mutagenesis was significantly detected abovebackground. FIG. 18A depicts a sequence alignment of CCR5 gRNAs utilizedin this study in relation to the closest homologous sequence in CCR2showing mismatched nucleotides in bold. Noteworthy is the fact thatguide crCCR5_B, which yielded the sole significantly detected off-targetmutagenesis in CCR2 (detailed in panel B), has 3 nucleotide mismatches,which are distal to the PAM (underlined) and seed (grey box) sequences.FIG. 18B is a Table depicting in-depth analyses of all sequence reads atthe single off-target site in which mutagenesis was significantlydetected above background in both capture libraries treated with theassociated gRNA (B; libraries treated with single gRNA crCCR5_B &dual-gRNA crCCR5_A+B), as well as the library treated with gRNA crCCR5_Aas a comparison. Total off-target mutation frequency at this site was0.6% in the single gRNA treatment (crCCR5_B) and notably decreased to0.24% in the dual gRNA treatment (crCCR5_A+B) in which gRNA plasmidconcentration of each gRNA was half of that utilized in single gRNAtreatments.

FIGS. 19A and 19B demonstrate the generation of Fgm knockout mice by aCRISPR/Cas system employing a modified Cas9 mRNA. FIG. 19A is aschematic illustrating the steps employed to generate Fgm knockout miceusing the CRISPR/Cas system employing the Cas9 modified RNA. FIG. 19Bshows part of a gel picture depicting results from PCR screening ofsurviving pups for genetic mutations resulting from genomic editingusing the CRISPR/Cas system and the modified Cas9 mRNA.

FIG. 20 shows predicted gRNA mapping in Ensembl GRCh37v71.

FIG. 21 shows guide pair crCCR5_A+B on-target alleles.

FIG. 22 shows guide pair crCCR5_C+D on-target alleles.

FIG. 23 shows guide pair crCCR5_D+Q on-target alleles.

FIG. 24 shows off-target sites with statistically significant mutationalburden.

FIG. 25 shows a comparison of on- and off-target mutational burdens.

DETAILED DESCRIPTION OF THE INVENTION

Work described herein demonstrates methods of allele targeting usingCRISPR/Cas systems resulting in mutant cells with efficiencies of up to80%. These vastly improved methods permit CRISPR/Cas systems to beutilized effectively for the first time for therapeutic purposes.Methods of delivery of CRISPR/Cas systems to human stem cells areprovided. In addition, methods of specifically identifying useful RNAguide sequences are provided, along with particular guide sequencesuseful in targeting specific genes (e.g., ADA, AK2, CD3D, DCLRE1C, HBB,IL2RG, IL7R, JAK3, LIG4, NHEJ1, PNP, PRKDC, RAG1, RAG2, and ZAP70).Moreover, methods of treatment (e.g., methods of treating severecombined immunodeficiency, sickle cell disease, and beta thalassemia)utilizing the compositions and methods disclosed herein are provided.

In one aspect, the present invention provides methods for alteringtarget polynucleotide sequences in a cell.

In certain embodiments, the target polynucleotide sequence is a severecombined immunodeficiency (SCID)-associated polynucleotide sequence. Insuch embodiments, a method for altering a target polynucleotide sequencein a cell comprises a method for altering a target SCID-associatedpolynucleotide sequence. As used herein, “severe combinedimmunodeficiency-associated polynucleotide sequence” and“SCID-associated polynucleotide sequence” are used interchangeably torefer to a polynucleotide sequence of a gene displaying one or moremutations associated with SCID. As used herein “severe combinedimmunodeficiency” and “SCID” refer to a genetic disorder characterizedby dysfunctional T-lymphocytes causing a defective antibody response dueto either a direct involvement with B lymphocytes or aberrant Blymphocyte activation resulting from non-functional T-helper cells. SCIDencompasses dysfunctional B and T cell responses of the adaptive immunesystem due to mutations in one or more genes, including, but not limitedto, ADA, AK2, CD3D, DCLRE1C, IL2RG, IL7R, JAK3, LIG4, NHEJ1, PNP, PRKDC,RAG1, RAG2, and ZAP70. As such, a “SCID-associated polynucleotidesequence” encompasses nucleotide sequences of any of these genes alongwith variant or mutant forms thereof.

An exemplary method for altering a target severe combinedimmunodeficiency (SCID)-associated polynucleotide sequence in a cellcomprises contacting the SCID-associated polynucleotide sequence with aclustered regularly interspaced short palindromic repeats-associated(Cas) protein and from one to two ribonucleic acids, wherein theribonucleic acids direct Cas protein to and hybridize to a target motifof the target SCID-associated polynucleotide sequence, wherein thetarget SCID associated polynucleotide sequence is cleaved. In someembodiments, the efficiency of alteration of cells that express Casprotein is from about 50% to about 80%.

In some embodiments, the SCID-associated polynucleotide sequence isadenosine deaminase (ADA) or a variant thereof. An exemplary ADAsequence is a human ADA sequence (NCBI Gene ID: 100). Those skilled inthe art will appreciate that the guide sequences shown in FIG. 1 can beused with the CRISPR/Cas systems of the present invention to altertarget polynucleotide sequences of human ADA.

It should also be appreciated that altering a target polynucleotidesequence of ADA can be used to treat any abnormal phenotype associatedwith an altered ADA polynucleotide sequence. Table 1 below shows genephenotype relationships identified by the Online Mendelian Inheritancein Man® (OMIM®) database. Further information regarding a phenotypelisted in Table 1 is publicly accessible by querying OMIM for the searchterm “ADA” and then clicking on a hyperlink in the “Phenotype MIMnumber” column corresponding to the phenotype listed.

TABLE 1 ADA Gene Phenotype Relationships Phenotype Location PhenotypeMIM number 20q13.12 Adenosine deaminase deficiency, partial 102700Severe combined immunodeficiency due 102700 to ADA deficiency

In some embodiments, the SCID-associated polynucleotide sequence isadenylate kinase 2 (AK2) or a variant thereof. An exemplary AK2 sequenceis a human AK2 sequence (NCBI Gene ID: 204, also known as ADK2 and AK2). In some embodiments, the human AK2 sequence comprises all or aportion of AK2 coding sequence 1. In some embodiments, the human AK2sequence comprises all or a portion of AK2 coding sequence 2. In someembodiments, the human AK2 sequence comprises all or a portion of AK2coding sequence 3. Those skilled in the art will appreciate that theguide sequences shown in FIGS. 2, 3 and 4 can be used with theCRISPR/Cas systems of the present invention to alter targetpolynucleotide sequences of human AK2, and in particular human AK2coding sequences 1, 2 and 3, respectively.

It should also be appreciated that altering a target polynucleotidesequence of AK2 can be used to treat any abnormal phenotype associatedwith an altered AK2 polynucleotide sequence. Table 2 below shows genephenotype relationships identified by the OMIM® database. Furtherinformation regarding a phenotype listed in Table 2 is publiclyaccessible by querying OMIM for the search term “AK2” and then clickingon a hyperlink in the “Phenotype MIM number” column corresponding to thephenotype listed.

TABLE 2 AK2 Gene Phenotype Relationships Phenotype Location PhenotypeMIM number 1p35.1 Reticular dysgenesis 267500

In some embodiments, the SCID-associated polynucleotide sequence is CD3antigen, delta subunit (CD3D) or a variant thereof. An exemplary CD3Dsequence is a human CD3D sequence (NCBI Gene ID: 915, also known as T3Dand CD3-DELTA). In some embodiments, the human CD3D sequence comprisesall or a portion of CD3D coding sequence 1. In some embodiments, thehuman CD3D sequence comprises all or a portion of CD3D coding sequence2. Those skilled in the art will appreciate that the guide sequencesshown in FIGS. 5 and 6 can be used with the CRISPR/Cas systems of thepresent invention to alter target polynucleotide sequences of humanCD3D, and in particular human CD3D coding sequences 1 and 2,respectively.

It should also be appreciated that altering a target polynucleotidesequence of CD3D can be used to treat any abnormal phenotype associatedwith an altered CD3D polynucleotide sequence. Table 3 below shows genephenotype relationships identified by the OMIM® database. Furtherinformation regarding a phenotype listed in Table 3 is publiclyaccessible by querying OMIM for the search term “CD3D” and then clickingon a hyperlink in the “Phenotype MIM number” column corresponding to thephenotype listed.

TABLE 3 CD3D Gene Phenotype Relationships Phenotype Location PhenotypeMIM number 11q23.3 Severe combined immunodeficiency, 608971 Tcell-negative, B-cell/natural killer-cell positive

In some embodiments, the SCID-associated polynucleotide sequence is DNAcross-link repair protein 1C (DCLRE1C) or a variant thereof. Anexemplary DCLRE1C sequence is a human DCLRE1C sequence (NCBI Gene ID:64421, also known as SCIDA, SNM1C, A-SCID, hSNM1C, RS-SCID, DCLRE1C). Insome embodiments, the human DCLRE1C sequence comprises all or a portionof DCLRE1C coding sequence 1. In some embodiments, the human DCLRE1Csequence comprises all or a portion of DCLRE1C coding sequence 2. Insome embodiments, the human DCLRE1C sequence comprises all or a portionof DCLRE1C coding sequence 3. In some embodiments, the human DCLRE1Csequence comprises all or a portion of DCLRE1C coding sequence 4. Thoseskilled in the art will appreciate that the guide sequences shown inFIGS. 7, 8, 9, and 10 can be used with the CRISPR/Cas systems of thepresent invention to alter target polynucleotide sequences of humanDCLRE1C, and in particular human DCLRE1C coding sequences 1, 2, 3, and4, respectively.

It should also be appreciated that altering a target polynucleotidesequence of DCLRE1C can be used to treat any abnormal phenotypeassociated with an altered DCLRE1C polynucleotide sequence. Table 4below shows gene phenotype relationships identified by the OMIM®database. Further information regarding a phenotype listed in Table 4 ispublicly accessible by querying OMIM for the search term “DCLRE1C” andthen clicking on a hyperlink in the “Phenotype MIM number” columncorresponding to the phenotype listed.

TABLE 4 DCLRE1C Gene Phenotype Relationships Phenotype LocationPhenotype MIM number 10p13 Omenn syndrome 603554 Severe combinedimmunodeficiency, 602450 Athabascan type

In some embodiments, the SCID-associated polynucleotide sequence isinterleukin 2 receptor, gamma (IL2RG) or a variant thereof. An exemplaryIL2RG sequence is a human IL2RG sequence (NCBI Gene ID: 3561, also knownas P64; CIDX; IMD4; CD132; SCIDX; IL-2RG; and SCIDX1). Those skilled inthe art will appreciate that the guide sequences shown in FIG. 12 can beused with the CRISPR/Cas systems of the present invention to altertarget polynucleotide sequences of human IL2RG.

It should also be appreciated that altering a target polynucleotidesequence of IL2RG can be used to treat any abnormal phenotype associatedwith an altered IL2RG polynucleotide sequence. Table 5 below shows genephenotype relationships identified by the OMIM® database. Furtherinformation regarding a phenotype listed in Table 5 is publiclyaccessible by querying OMIM for the search term “IL2RG” and thenclicking on a hyperlink in the “Phenotype MIM number” columncorresponding to the phenotype listed.

TABLE 5 IL2RG Gene Phenotype Relationships Phenotype Location PhenotypeMIM number Xq13.1 Combined immunodeficiency, X-linked, moderate 312863Severe combined immunodeficiency, X-linked 300400

In some embodiments, the SCID-associated polynucleotide sequence isinterleukin 7 receptor (IL7R) or a variant thereof. An exemplary IL7Rsequence is a human IL7R sequence (NCBI Gene ID: 3575, also known asILRA, CD127, IL7RA, CDW127, IL-7R-alpha). Those skilled in the art willappreciate that the guide sequences shown in FIG. 13 can be used withthe CRISPR/Cas systems of the present invention to alter targetpolynucleotide sequences of human IL7R.

It should also be appreciated that altering a target polynucleotidesequence of IL7R can be used to treat any abnormal phenotype associatedwith an altered IL7R polynucleotide sequence. Table 6 below shows genephenotype relationships identified by the OMIM® database. Furtherinformation regarding a phenotype listed in Table 6 is publiclyaccessible by querying OMIM for the search term “IL7R” and then clickingon a hyperlink in the “Phenotype MIM number” column corresponding to thephenotype listed.

TABLE 6 IL7R Gene Phenotype Relationships Phenotype Location PhenotypeMIM number 5p13.2 Severe combined immunodeficiency, 608971 T-cellnegative, B-cell/natural killer cell-positive type

In some embodiments, the SCID-associated polynucleotide sequence isJanus kinase 3(JAK3) or a variant thereof. An exemplary JAK3 sequence isa human JAK3 sequence (NCBI Gene ID: 3718, also known as JAKL; LJAK;JAK-3; L-JAK; JAK3_HUMAN). Those skilled in the art will appreciate thatthe guide sequences shown in FIG. 14 can be used with the CRISPR/Cassystems of the present invention to alter target polynucleotidesequences of human JAK3.

It should also be appreciated that altering a target polynucleotidesequence of JAK3 can be used to treat any abnormal phenotype associatedwith an altered JAK3 polynucleotide sequence. Table 7 below shows genephenotype relationships identified by the OMIM® database. Furtherinformation regarding a phenotype listed in Table 7 is publiclyavailable by querying OMIM for the search term “JAK3” and then clickingon a hyperlink in the “Phenotype MIM number” column corresponding to thephenotype listed.

TABLE 7 JAK3 Gene Phenotype Relationships Phenotype Location PhenotypeMIM number 19p13.11 SCID, autosomal recessive, 600802T-negative/B-positive type

In some embodiments, the SCID-associated polynucleotide sequence isligase IV, DNA, ATP-dependent (LIG4) or a variant thereof. An exemplaryLIG4 sequence is a human LIG4 sequence (NCBI Gene ID: 3981). In someembodiments, the human LIG4 sequence comprises all or a portion of LIG4coding sequence 1. In some embodiments, the human LIG4 sequencecomprises all or a portion of LIG4 coding sequence 2. In someembodiments, the human LIG4 sequence comprises all or a portion of LIG4coding sequence 3. Those skilled in the art will appreciate that theguide sequences shown in FIGS. 15, 16, and 17 can be used with theCRISPR/Cas systems of the present invention to alter targetpolynucleotide sequences of human LIG4, and in particular human LIG4coding sequences 1, 2, and 3, respectively.

It should also be appreciated that altering a target polynucleotidesequence of LIG4 can be used to treat any abnormal phenotype associatedwith an altered LIG4 polynucleotide sequence. Table 8 below shows genephenotype relationships identified by the OMIM® database. Furtherinformation regarding a phenotype listed in Table 8 is publiclyaccessible by querying OMIM for the search term “LIG4” and then clickingon a hyperlink in the “Phenotype MIM number” column corresponding to thephenotype listed.

TABLE 8 LIG4 Gene Phenotype Relationships Phenotype Location PhenotypeMIM number 13q33.3 LIG4 syndrome 606593 Severe combined immunodeficiencywith 602450 sensitivity to ionizing radiation {Multiple myeloma,resistance to} 254500

In some embodiments, the SCID-associated polynucleotide sequence isnonhomologous end-joining factor 1 (NHEJ1) or a variant thereof. Anexemplary NHEJ1 sequence is the human NHEJ1 sequence (NCBI Gene ID:79840, also known as XLF). Those skilled in the art will appreciate thatthe guide sequences shown in FIG. 18 can be used with the CRISPR/Cassystems of the present invention to alter target polynucleotidesequences of human NHEJ1.

It should also be appreciated that altering a target polynucleotidesequence of NHEJ1 can be used to treat any abnormal phenotype associatedwith an altered NHEJ1 polynucleotide sequence. Table 9 below shows genephenotype relationships identified by the OMIM® database. Furtherinformation regarding a phenotype listed in Table 9 is publiclyaccessible by querying OMIM for the search term “NHEJ1” and thenclicking on a hyperlink in the “Phenotype MIM number” columncorresponding to the phenotype listed.

TABLE 9 NHEJ1 Gene Phenotype Relationships Phenotype Location PhenotypeMIM number 2q35 Severe combined immunodeficiency with 611291microcephaly, growth retardation, and sensitivity to ionizing radiation

In some embodiments, the SCID-associated polynucleotide sequence is apurine nucleoside phosphorylase sequence (PNP) or a variant thereof. Anexemplary PNP sequence is human PNP (NCBI Gene ID: 4860, also known asNP, PUNP, and PR01837). Those skilled in the art will appreciate thatthe guide sequences shown in FIG. 19 can be used with the CRISPR/Cassystems of the present invention to alter target polynucleotidesequences of human PNP.

It should also be appreciated that altering a target polynucleotidesequence of PNP can be used to treat any abnormal phenotype associatedwith an altered PNP polynucleotide sequence. Table 10 below shows genephenotype relationships identified by the OMIM® database. Furtherinformation regarding a phenotype listed in Table 10 is publiclyaccessible by querying OMIM for the search term “PNP” and then clickingon a hyperlink in the “Phenotype MIM number” column corresponding to thephenotype listed.

TABLE 10 PNP Gene Phenotype Relationships Phenotype Location PhenotypeMIM number 14q11.2 Immunodeficiency due to purine nucleoside 613179phosphorylase deficiency

In some embodiments, the SCID-associated polynucleotide sequence is aprotein kinase, DNA activated, catalytic polypeptide sequence (PRKDC) ora variant thereof. An exemplary PRKDC sequence is human PRKDC (NCBI GeneID: 5591, also known as HYRC; p350; DNAPK; DNPK1; HYRC1; XRCC7; andDNA-PKcs). In some embodiments, the human PRKDC sequence comprises allor a portion of PRKDC coding sequence 1. In some embodiments, the humanPRKDC sequence comprises all or a portion of PRKDC coding sequence 2.Those skilled in the art will appreciate that the guide sequences shownin FIGS. 20 and 21 can be used with the CRISPR/Cas systems of thepresent invention to alter target polynucleotide sequences of humanPRKDC, and in particular human PRKDC coding sequences 1 and 2,respectively.

It should also be appreciated that altering a target polynucleotidesequence of PRKDC can be used to treat any abnormal phenotype associatedwith an altered PRKDC polynucleotide sequence. In some embodiments, thephenotype associated with an altered PRKDC polynucleotide sequence isSCID. In some embodiments, the phenotype associated with an alteredPRKDC polynucleotide sequence is radiosensitivity in xerodermapigmentosum (Abbaszadeh et al., A novel splice variant of the DNA-PKcsgene is associated with clinical and cellular radiosensitivity in apatient with xeroderma pigmentosum. J Med Genet. 2010; 47(3):176-81).

In some embodiments, the SCID-associated polynucleotide sequence is arecombination activating gene 1 sequence (RAG1) or a variant thereof. Anexemplary RAG1 sequence is human RAG1 (NCBI Gene ID: 5896, also known asRAG-1 and RNF74). Those skilled in the art will appreciate that theguide sequences shown in FIG. 22 can be used with the CRISPR/Cas systemsof the present invention to alter target polynucleotide sequences ofhuman RAG1.

It should also be appreciated that altering a target polynucleotidesequence of RAG1 can be used to treat any abnormal phenotype associatedwith an altered RAG1 polynucleotide sequence. Table 11 below shows genephenotype relationships identified by the OMIM® database. Furtherinformation regarding a phenotype listed in Table 11 is publiclyaccessible by querying OMIM for the search term “RAG1” and then clickingon a hyperlink in the “Phenotype MIM number” column corresponding to thephenotype listed.

TABLE 11 RAG1 Gene Phenotype Relationships Phenotype Location PhenotypeMIM number 11p12 Alpha/beta T-cell lymphopenia with 609889 gamma/deltaT-cell expansion, severe cytomegalovirus infection, and autoimmunityCombined cellular and humoral 233650 immune defects with granulomasOmenn syndrome 603554 Severe combined immunodeficiency, 601457 Bcell-negative

In some embodiments, the SCID-associated polynucleotide sequence is arecombination activating gene 2 sequence (RAG2) or a variant thereof. Anexemplary RAG2 sequence is human RAG2 (NCBI Gene ID: 5897, also known asRAG-2). In some embodiments, the human RAG2 sequence comprises all or aportion of human RAG2 coding sequence 1. In some embodiments, the humanRAG2 sequence comprises all or a portion of human RAG2 coding sequence2. In some embodiments, the human RAG2 sequence comprises all or aportion of human RAG2 coding sequence 3. Those skilled in the art willappreciate that the guide sequences shown in FIGS. 23, 24 and 25 can beused with the CRISPR/Cas systems of the present invention to altertarget polynucleotide sequences of human RAG2, and in particular humanRAG2 coding sequences 1, 2 and 3, respectively.

It should also be appreciated that altering a target polynucleotidesequence of RAG2 can be used to treat any abnormal phenotype associatedwith an altered RAG2 polynucleotide sequence. Table 12 below shows genephenotype relationships identified by the OMIM® database. Furtherinformation regarding a phenotype listed in Table 12 is publiclyaccessible by querying OMIM for the search term “RAG2” and then clickingon a hyperlink in the “Phenotype MIM number” column corresponding to thephenotype listed.

TABLE 12 RAG2 Gene Phenotype Relationships Phenotype Location PhenotypeMIM number 11p12 Combined cellular and humoral 233650 immune defectswith granulomas Omenn syndrome 603554 Severe combined immunodeficiency,601457 B cell-negative

In some embodiments, the SCID-associated polynucleotide sequence is azeta-chain-associated protein kinase sequence (ZAP70) or a variantthereof. An exemplary ZAP70 sequence is human ZAP70 (NCBI Gene ID: 7535,also known as SRK; STD; TZK; STCD; and ZAP-70). In some embodiments, thehuman ZAP70 sequence comprises all or a portion of human ZAP70 codingsequence 1. In some embodiments, the human ZAP70 sequence comprises allor a portion of human ZAP70 coding sequence 2. Those skilled in the artwill appreciate that the guide sequences shown in FIGS. 26 and 27 can beused with the CRISPR/Cas systems of the present invention to altertarget polynucleotide sequences of human ZAP70, and in particular humanZAP70 coding sequences 1 and 2, respectively.

It should also be appreciated that altering a target polynucleotidesequence of ZAP70 can be used to treat any abnormal phenotype associatedwith an altered ZAP70 polynucleotide sequence. Table 13 below shows genephenotype relationships identified by the OMIM® database. Furtherinformation regarding a phenotype listed in Table 13 is publiclyaccessible by querying OMIM for the search term “ZAP70” and thenclicking on a hyperlink in the “Phenotype MIM number” columncorresponding to the phenotype listed.

TABLE 13 ZAP 70 Gene Phenotype Relationships Phenotype LocationPhenotype MIM number 2q11.2 Selective T-cell defect 269840

In some embodiments, the target polynucleotide sequence is hemoglobinbeta (“HBB”) (e.g., human hemoglobin beta, NCBI Gene ID: 3043) or avariant thereof. Those skilled in the art will appreciate that the guidesequences shown in FIG. 11 can be used with the CRISPR/Cas systems ofthe present invention to alter target polynucleotide sequences of humanHBB.

It should also be appreciated that altering a target polynucleotidesequence of HBB can be used to treat any abnormal phenotype associatedwith an altered HBB polynucleotide sequence. Table 14 below shows genephenotype relationships as identified by the OMIM® database. Furtherinformation regarding a phenotype listed in Table 14 is publiclyaccessible by querying OMIM for the search term “HBB” and then clickingon a hyperlink in the “Phenotype MIM number” column corresponding to thephenotype listed.

TABLE 14 HBB Gene Phenotype Relationships Phenotype Location PhenotypeMIM number 11p15.4 Delta-beta thalassemia 141749 Erythremias, beta-Heinz body anemias, beta- 140700 Hereditary persistence of fetalhemoglobin 141749 Methemoglobinemias, beta- Sickle cell anemia 603903Thalassemia-beta, dominant inclusion-body 603902 Thalassemias, beta-613985 {Malaria, resistance to} 611162

Normal adult hemoglobin is a tetramer that consists of two alpha chainsand two beta chains. HBB determines the structure of the beta chains ofhemoglobin. HBB mutations are associated with sickle cell diseasesand/or beta thalassemia. For example, sickle cell anemia is caused bymutant beta globin. The absence of the beta chain results in beta-zerothalassemia. Diminished amounts of detectable beta globin results inbeta-plus-thalassemia. Exemplary mutant forms of HBB involved in sicklecell disease are Hemoglobin S (Glu6Val), Hemoglobin C (Glu6Lys),Hemoglobin D (Glu121Gln), and Hemoglobin O (Glu121Lys).

Insertion of an L1 retrotransposable fragment within the IVS-II of thebeta-globin gene results in beta^(∘)-thal. This represents a form ofbeta thalassemia in which the beta globin gene expresses full lengthbeta-globin transcripts at levels equal to about 15% of the totalbeta-globin mRNA.

In some embodiments, a method for altering a target polynucleotidesequence in a cell comprises a method for altering a target sickle celldisease (SCD)-associated polynucleotide sequence. As used herein,“sickle cell disease-associated polynucleotide sequence” or“SCD-associated polynucleotide sequence” are used interchangeably torefer to a polynucleotide sequence of the HBB gene displaying one ormore HBB mutations associated with SCD. As used herein, “sickle celldisease” refers to a group of symptomatic disorders involving mutationsin HBB and defined by the presence of hemoglobin S (Hb S). Normalhemoglobin is a heterotetramer consisting of two alpha-hemoglobin andtwo beta-hemoglobin chains. Point mutations in HBB cause hemoglobin S toresult, for example a point mutation changing the sixth amino acid inthe beta-hemoglobin chain from glutamic acid to valine (Glu6Val). Sicklecell anemia (homogzygous HbSS) is an example of a sickle cell diseasewhich makes up between 60-70% of reported sickle cell disease in theUnited States. Examples of other forms of sickle cell disease are due tocoinhereitance of Hb S with various mutant beta-globin chain variants,including sickle-hemoglobin C disease (Hb SC), and two different typesof sickle beta thalassemia (Hb Sβ⁺_thalassemia and Hb S Pβ_thalassemia).

An exemplary method for altering a target sickle cell disease(SCD)-associated polynucleotide sequence in a cell comprises contactingthe SCD-associated polynucleotide sequence with a clustered regularlyinterspaced short palindromic repeats-associated (Cas) protein and fromone to two ribonucleic acids, wherein the ribonucleic acids direct Casprotein to and hybridize to a target motif of the target SCD-associatedpolynucleotide sequence, wherein the target SCD-associatedpolynucleotide sequence is cleaved. In some embodiments of this andother aspects, the efficiency of alteration of cells that express Casprotein is from about 50% to about 80%.

In some embodiments, a method for altering a target polynucleotidesequence in a cell comprises a method for altering a target betathalassemia-associated polynucleotide sequence. As used herein, “betathalassemia-associated polynucleotide sequence” refers to apolynucleotide sequence of the HBB gene displaying one or more HBBmutations associated with beta thalassemia. As used herein, “betathalassemia” refers to inherited autosomal recessive diseasescharacterized by decreased production of the hemoglobin subunit beta(e.g., hemoglobin beta chain) that are caused by over 200 different HBBmutations. As will be appreciated by the skilled artisan, HBB mutationsresulting in beta thalassemia include non-deletional HBB mutants,deletional HBB mutants, and HBB mutants resulting from transposableelements. Table 15 below illustrates exemplary non-deletional HBBmutations.

TABLE 15 Non-deletional HBB mutations associated with beta thalassemia−101 (C−>T) −92 (C−>T) −90 (C−>T) −88 (C−>A) −88 (C−>T) −87 (C−>A) −87(C−>G) −87 (C−>T) −86 (C−>A) −86 (C−>G) −32 (C−>A) −31 (A−>C) −31 (A−>G)−30 (T−>A) −30 (T−>C) −29 (A−>G) −28 (A−>C) −28 (A−>G) CAP +1(A−>C)5′UTR; +10(−T) 5′UTR; +22 (G−>A) 5′UTR; +33 (C−>G) 5′UTR; +43 to+40(−AAAC) Initiation codon ATG−>GTG Initiation codon ATG−>ACGInitiation codon ATG−>AGG Initiation codon ATG−>ATA Initiation codonATG−>ATC Initiation codon ATG−>ATT Codon 1 (−G); GTG(Val)−>−TG Codons2/3/4 (−9 bp; +31 bp); (see below) Codon 5 (−CT); CCT(Pro)−>C-- Codon 6(−A); GAG(Glu)−>G-G Codon 8 (−AA); AAG(Lys)−>--G Codons 8/9 (+G); AAG.TCT(Lys; Ser)−>AAG•G•TCT Codons 9/10 (+T); TCT•GCC(Ser; Ala)−>TCT•T•GCCCodon 10 (C−>A); GCC(Ala)−>GCA(Ala) Codon 11 (−T); GTT(Val)−>GT- Codons14/15 (+G); Codon 15 (G−>A); TGG(Trp)−>TAG(stop codon) Codon 15 (G−>A);TGG(Trp)−>TGA(stop codon) Codon 15 (−T); TGG(Trp)−>−GG Codon 16 (−C);GGC(Gly)−>GG- Codon 17 (A−>T); AAG(Lys)−>TAG(stop codon) Codon 19(A−>G); AAC(Asn)−>AGC(Ser) Codon 22 (A−>C); GAA(Glu)−>GCA(Ala) (notlisted in Table I; this mutation is likely not associated withthalassemia) Codon 22 (G−>T); GAA(Glu)−>TAA(stop codon) Codons 22/23/24(GAA•GTT•GGT; Glu•Val•Gly); deletion of −AAGTTGG Codon 24; GGT(Gly);(−G; +CAC) Codon 24 (T−>A); GGT(Gly)−>GGA(Gly) Codons 24/25 (−GGT);GGT•GGT(Gly-Gly)−>---•GGT(Gly) Codons 25/26 (+T);GGT•GAG(Gly-Glu)−>GGT•T•GAG(Gly-Term) Codon 26 (GAG−>AAG) Codon 26(G−>T); GAG(Glu)−>TAG(stop codon) Codon 26 (+T); GAG(Glu)−>GTAG Codon 27(G−>T); GCC(Ala)−>TCC(Ser) Codons 27/28 (+C);GCC•CTG(Ala•Ser)−>GCC•C•CTG Codon 28 (−C); CTG(Leu)−>−TG Codon 28(T−>G); CTG(Leu)−>CGG(Arg) Codons 28/29 (−G); CTG•GGC(Leu•Gly)−>CTG•−GCIVS-I (−3) or codon 29 (C−>T); GGC(Gly)−>GGT(Gly) IVS-I (−2) or codon 30(A−>G); AG{circumflex over ( )}GTTGGT−>GG{circumflex over ( )}GTTGGTIVS-I (−1) or codon 30 (G−>A); AG{circumflex over( )}GTTGGT−>AA{circumflex over ( )}GTTGGT IVS-I (−1) or codon 30 (G−>C);AG{circumflex over ( )}GTTGGT−>AC{circumflex over ( )}GTTGGT IVS-I-1(G−>A); AG{circumflex over ( )}GTTGGT−>AGATTGGT IVS-I-1 (G−>T);AG{circumflex over ( )}GTTGGT−>AGTTTGGT IVS-I-2 (T−>A); AG{circumflexover ( )}GTTGGT−>AGGATGGT IVS-I-2 (T−>C); AG{circumflex over( )}GTTGGT−>AGACTGGT IVS-I-2 (T−>G); AG{circumflex over( )}GTTGGT−>AGGGTGGT IVS-I-5 (G−>A) IVS-I-5 (G−>A) plus the 7,201 bpdeletion involving part of the delta gene; the Corfu deletion(deltabeta-thal) IVS-I-5 (G−>C) IVS-I-5 (G−>T) IVS-I-6 (T−>C); thePortuguese type IVS-I-110 (G−>A) IVS-I-116 (T−>G) IVS-I-128 (T−>G);TTAG{circumflex over ( )}GCTG−>TGAG{circumflex over ( )}GCTG IVS-I-130(G−>A); TTAG{circumflex over ( )}GCTG−>TTAA{circumflex over ( )}GCTGIVS-I-130 (G−>C); TTAG{circumflex over ( )}GCTG−>TTAC{circumflex over( )}GCTG Codon 30 (AGG−>AGC) [IVS-I-130 (+1)] IVS-I, 3′ end; −17 bpCodon 31 (−C); CTG−>−TG Codons 31/32 (+CGG) Codon 32 (T−>A) CTG−>CAG;codon 98 (G−>A) GTG−>ATG Codons 33/34 (−GTG);GTG•GTC(Val-Val)−>GTC•---(Val) Codon 35 (C−>A); TAC−>TAA (Tyr−>Termcodon) Codon 35 (−C); TAC(Tyr)−>TA- Codons 36/37 (−T);CCT•TGG(Pro-Trp)−>CCT•−GG Codon 37 (G−>A); TGG(Trp)−>TGA(stop codon)Codons 37/38/39 (−7 nts) Codons 38/39 (−C); ACC•CAG(Thr•Gln)−>ACC•−AGCodons 38/39 (−CC); ACC•CAG(Thr-Glu)−>A--•CAG Codon 39 (C−>T);CAG(Gln)−>TAG(stop codon) Codon 40 (−G); AGG(Arg)−>AG- Codons 40/41(+T); AGG•TTC(Arg-Phe)−>AGG•T•TTC Codon 41 (−C); TTC(Phe)−>TT- Codons41/42 (−TTCT); TTC•TTT(Phe-Phe)−>--- −TT Codons 42/43 (+G);TTT•GAG(Phe•Glu)−>TTT•G•GAG Codons 42/43 (+T)TTT•GAG(Phe•Glu)−>TTT•TGA•G(Phe; stop codon) Codon 43 (G−>T);GAG(Glu)−>TAG (stop codon) Codon 44 (−C); TCC(Ser)−>TC- Codon 45 (−T);TTT(Phe)−>−TT Codon 47 (+A); GAT(Asp)−>GAA(Glu)•T Codons 47/48 (+ATCT);GAT•CTG(Asp-Leu)−>GAT•CTATCTG Codon 51 (−C); CCT(Pro)−>−CT 53/54 (+G);GCT•GTT(Ala-Val)−>GCT•G•GTT Codon 54 (−T); GTT(Val)−>GT- Codons 54/55(+A); GTT•ATG(Val•Met)−>GTT•A•ATG Codons 56/57/58/59/60(GGC•AAC•CCT•AAG•GTG) (SEQ ID NO: 5345); duplication of 14 bp Codons57/58 (+C); AAC•CCT(Asn•Pro)−>AAC•C•CCT Codon 59 (−A); AAG(Lys)−>−AGCodon 60 (T−>A); GTG(Val)−>GAG(Glu) Codon 61 (A−>T); AAG(Lys)−>TAG(stopcodon) Codon 64 (−G); GGC(Gly)−>−GC Codon 67 (−TG); GTG(Val)−>--G Codons71/72 (+A); TTT•AGT(Phe•Ser)−>TTT•A•AGT Codons 71/72 (+T);TTT•AGT(Phe•Ser)−>TTT•T•AGT Codons 72/73; −AGTGA, +T;AGT•GAT(Ser-Asp)−>--- −TT Codons 74/75 (−C); GGC•CTG(Gly• Leu)−>GG--CTGCodon 76 (−C); GCT(Ala)−>G−T Codons 82/83 (−G);AAG•GGC(Lys•Gly)−>AAG•−GC Codons 84/85 (+C); ACC•TTT(Thr•Phe)−>ACC•C•TTT Codons 84/85/86 (+T);ACC•TTT•GCC(Thr•Phe•Ala)−>ACC•TTT•T•GCC Codon 88 (+T); CTG(Leu)−>CTTGCodons 89/90 (−GT); AGT•GAG(Ser•Glu)−>A--•GAG Codon 90 (G−>T);GAG(Glu)−>TAG(stop codon) Codon 94 (+TG); GAC(Asp)−>GTGAC Codon 95 (+A);AAG(Lys)−>AAAG Codon 100; −CTT, +TCTGAGAACTT IVS-II-1 (G−>A); IVS-II-1(G−>C); IVS-II-2,3 (+11, −2); insertion of 11 bp (5′-ACGTTCT CTGA-3′)(SEQ ID NO: 5346) and deletion of GA (nts 2 and 3 of IVS-II) betweenpositions 1 and 4 of IVS-II IVS-II-4,5 (−AG); IVS-II-5 (G−>C) IVS-II-654(C−>T); AAGGCAATA−>AAG{circumflex over ( )}GTAATA IVS-II-705 (T−>G);GATGTAAGA−>GAG{circumflex over ( )}GTAAGA IVS-II-745 (C−>G);CAGCACCAT−>CAG{circumflex over ( )}GTACCAT IVS-II-837 (T−>G); IVS-II-843(T−>G); IVS-II-844 (C−>G); IVS-II-848 (C−>A); IVS-II-848 (C−>G);IVS-II-849 (A−>C); IVS-II-849 (A−>G); IVS-II-850 (−G); IVS-II-850(G−>A); IVS-II-850 (G−>C); IVS-II-850 (G−>T); Codons 106/107 (+G);CTG•GGC(Leu•Gly)−>CTG•G•GC Codons 108/109/110/111/112 (−12 bp); Codon109 (−G); GTG(Val)−>−TG Codon 110 (T−>C); CTG(Leu)−>CCG(Pro) Codon 112(T−>A); TGT(Cys)−>TGA(stop codon) Codon 114 (T−>C); CTG(Leu)−>CCG(Pro)Codon 114 (−CT; +G); CTG(Leu)−>−GG Codon 115 (C−>A); GCC(Ala)−>GAC(Asp)Codons 120/121 (+A); AAA•GAA(Lys-Glu)−>AAA•A•GAA Codon 121 (G−>T);GAA(Glu)−>TAA(stop codon) Codon 123 (−A); ACC(Thr)−>−CC Codons123/124/125 (−ACCCCACC); ACC•CCA•CCA(Thr•Pro•Pro)−>--- --- --A Codon 124(−A); CCA(Pro)−>CC- Codon 125 (−A); CCA(Pro)−>CC− Codons 124/125/126(+CCA); CCA•CCA•GTG(Pro•Pro•Val) (SEQ ID NO: 5347)- >CCA•CCA•CCA•GTG(Pro•Pro•Pro•Val) (SEQ ID NO: 5348) Codon 126 (−T); GTG(Val)−>G−G Codon126 (T−>G); GTG(Val)−>GGG(Gly) Codons 126-131 (Val-Gln-Ala-Ala-Thr-Gln(SEQ ID NO: 5349)) (−17 bp); GTG•GAG•GCT•GCC•TAT•CAG (SEQ ID NO: 5350)−>G Codon 127 (A−>C); CAG(Gln)−>CCG(Pro) Codon 127 (A−>G);CAG(Gln)−>CGG(Arg) Codon 127 (C−>T); CAG(Gln)−>TAG(stop codon) Codons127/128 (−AGG); CAG•GCT(Gln•Ala)−>C-- −CT(Pro) Codons 128/129 (−4 bp,−GCTG; +5 bp, +CCACA) Codons 132-135 (−11 bp, −AAAGTGGTGGC) (SEQ ID NO:5351) Codons 134/135/136/137 [−(G)TGGCTGGTGT(G) (SEQ ID NO: 5352) and+(G)GCAG(G)]; GTG•GCT•GGT•GTG (SEQ ID NO: 5353) (Val-Ala-Gly-Val) (SEQID NO: 5354) −>GGC•AGG(Gly-Arg) +1480 (C−>G); also known as 3′terminating codon +6 (C−>G) 3′ UTR (−GCATCTGGATTCT) (SEQ ID NO: 5355) 13bp deletion between positions +1565 to +1577 (the numbers are relativeto the Cap site) T−>C; 12 nts 5′ to the poly A site or +1570 (the numberis relative to the Cap site) Poly A (T−>C); AATAAA−>AACAAA Poly A(A−>G); AATAAA−>AATGAA Poly A (A−>G); AATAAA−>AATAGA Poly A (A−>G);AATAAA−>AATAAG Poly A (−AT or −TA); AATAAA−>A--AAA Poly A (−AATAA);AATAAA−>-----A

Those skilled in the art will also appreciate that a variety ofdeletional beta thalassemia alleles exist, which tend to be prevalent incertain at-risk populations. Examples of such deletional betathalassemia alleles include, but are not limited to, a 25 bp deletion, a44 bp deletion, a 105 bp deletion, a 290 bp deletion, a 532 bp deletion,a 619 bp deletion, a 1,393 bp deletion, a 1,605 bp deletion (“Croatiandeletion”), a 3,485 bp deletion (“Thai deletion”), a 4,237 bp deletion(“Czech deletion”), a 7.6 kb deletion (“Turkish deletion”); a 10,329 bpdeletion (“Asian Indian deletion”), a 12,023 bp deletion (“Australiandeletion”); a 12,620 bp deletion (“Dutch deletion”), a 27 kb deletion(“Southeast Asian deletion”), a 45 kb deletion (“Filipino deletion”),and a 65 kb deletion (“Italian deletion”). Those skilled in the art willbe able to retrieve the corresponding nucleic acid and protein sequencescorresponding to these deletions from publicly available sources (e.g.,A Syllabus of Thalassemia Mutations (1997) by Titus H. J. Huisman, etal. published by The Sickle Cell Anemia Foundation in Augusta, Ga., USA,available online athttp://globin.cse.psu.edu/html/huisman/thals/I-b.entries.html).

An exemplary method for altering a target beta thalassemia-associatedpolynucleotide sequence in a cell comprises contacting the betathalassemia-associated polynucleotide sequence with a clusteredregularly interspaced short palindromic repeats-associated (Cas) proteinand from one to two ribonucleic acids, wherein the ribonucleic acidsdirect Cas protein to and hybridize to a target motif of the target betathalassemia-associated polynucleotide sequence, wherein the target betathalassemia associated polynucleotide sequence is cleaved. In someembodiments of this and other aspects, the efficiency of alteration ofcells that express Cas protein is from about 50% to about 80%.

As used herein, the term “contacting” (i.e., contacting a polynucleotidesequence with a clustered regularly interspaced short palindromicrepeats-associated (Cas) protein and/or ribonucleic acids) is intendedto include incubating the Cas protein and/or the ribonucleic acids inthe cell together in vitro (e.g., adding the Cas protein or nucleic acidencoding the Cas protein to cells in culture). In some embodiments, theterm “contacting” is not intended to include the in vivo exposure ofcells to the Cas protein and/or ribonucleic acids as disclosed hereinthat may occur naturally in a microorganism (i.e., bacteria). The stepof contacting a target polynucleotide sequence with a Cas protein and/orribonucleic acids as disclosed herein can be conducted in any suitablemanner. For example, the cells may be treated in adherent culture, or insuspension culture. It is understood that the cells contacted with a Casprotein and/or ribonucleic acids as disclosed herein can also besimultaneously or subsequently contacted with another agent, such as agrowth factor or other differentiation agent or environments tostabilize the cells, or to differentiate the cells further.

In another aspect, the present invention provides a method for treatingor preventing a disorder associated with expression of a polynucleotidesequence in a subject.

The terms “treat”, “treating”, “treatment”, etc., as applied to anisolated cell, include subjecting the cell to any kind of process orcondition or performing any kind of manipulation or procedure on thecell. As applied to a subject, the terms refer to providing medical orsurgical attention, care, or management to an individual. The individualis usually ill or injured, or at increased risk of becoming ill relativeto an average member of the population and in need of such attention,care, or management.

As used herein, the term “treating” and “treatment” refers toadministering to a subject an effective amount of a composition so thatthe subject has a reduction in at least one symptom of the disease or animprovement in the disease, for example, beneficial or desired clinicalresults. For purposes of this invention, beneficial or desired clinicalresults include, but are not limited to, alleviation of one or moresymptoms, diminishment of extent of disease, stabilized (i.e., notworsening) state of disease, delay or slowing of disease progression,amelioration or palliation of the disease state, and remission (whetherpartial or total), whether detectable or undetectable. Treating canrefer to prolonging survival as compared to expected survival if notreceiving treatment. Thus, one of skill in the art realizes that atreatment may improve the disease condition, but may not be a completecure for the disease. As used herein, the term “treatment” includesprophylaxis. Alternatively, treatment is “effective” if the progressionof a disease is reduced or halted. “Treatment” can also mean prolongingsurvival as compared to expected survival if not receiving treatment.Those in need of treatment include those already diagnosed with adisorder associated with expression of a polynucleotide sequence, aswell as those likely to develop such a disorder due to geneticsusceptibility or other factors.

By “treatment”, “prevention” or “amelioration” of a disease or disorderis meant delaying or preventing the onset of such a disease or disorder,reversing, alleviating, ameliorating, inhibiting, slowing down orstopping the progression, aggravation or deterioration the progressionor severity of a condition associated with such a disease or disorder.In one embodiment, the symptoms of a disease or disorder are alleviatedby at least 5%, at least 10%, at least 20%, at least 30%, at least 40%,or at least 50%.

In some embodiments, a method for treating or preventing a disorderassociated with expression of a polynucleotide sequence comprises amethod for treating or preventing a disorder associated with expressionof a SCID-associated polynucleotide sequence.

An exemplary method for treating or preventing a disorder associatedwith expression of a SCID-associated polynucleotide sequence in asubject comprises (a) altering a target SCID-associated polynucleotidesequence in a cell ex vivo by contacting the SCID-associatedpolynucleotide sequence with a clustered regularly interspaced shortpalindromic repeats-associated (Cas) protein and from one to tworibonucleic acids, wherein the ribonucleic acids direct Cas protein toand hybridize to a target motif of the target SCID-associatedpolynucleotide sequence, wherein the target SCD-associatedpolynucleotide sequence is cleaved, and (b) introducing the cell intothe subject, thereby treating or preventing a disorder associated withexpression of the SCID-associated polynucleotide sequence. In someembodiments of this and other aspects, the efficiency of alteration ofcells that express Cas protein is from about 50% to about 80%.

An exemplary method for treating or preventing a disorder associatedwith expression of a SCID-associated polynucleotide sequence in asubject comprises altering a target SCID-associated polynucleotidesequence in a cell by contacting the SCID-associated polynucleotidesequence with a clustered regularly interspaced short palindromicrepeats-associated (Cas) protein and from one to two ribonucleic acids,wherein the ribonucleic acids direct Cas protein to and hybridize to atarget motif of the target SCID-associated polynucleotide sequence, andwherein the target SCID-associated polynucleotide sequence is cleaved,thereby treating or preventing a disorder associated with expression ofthe SCID-associated polynucleotide sequence.

In some embodiments, a method for treating or preventing a disorderassociated with expression of a polynucleotide sequence comprises amethod for treating or preventing a disorder associated with expressionof a SCD-associated polynucleotide sequence.

An exemplary method for treating or preventing a disorder associatedwith expression of a SCD-associated polynucleotide sequence in a subjectcomprises (a) altering a target SCD-associated polynucleotide sequencein a cell ex vivo by contacting the SCD-associated polynucleotidesequence with a clustered regularly interspaced short palindromicrepeats-associated (Cas) protein and from one to two ribonucleic acids,wherein the ribonucleic acids direct Cas protein to and hybridize to atarget motif of the target SCD-associated polynucleotide sequence,wherein the target SCD-associated polynucleotide sequence is cleaved,and (b) introducing the cell into the subject, thereby treating orpreventing a disorder associated with expression of the SCD-associatedpolynucleotide sequence. In some embodiments of this and other aspects,the efficiency of alteration of cells that express Cas protein is fromabout 50% to about 80%.

An exemplary method for treating or preventing a disorder associatedwith expression of a SCD-associated polynucleotide sequence in a subjectcomprises altering a target SCD-associated polynucleotide sequence in acell by contacting the SCD-associated polynucleotide sequence with aclustered regularly interspaced short palindromic repeats-associated(Cas) protein and from one to two ribonucleic acids, wherein theribonucleic acids direct Cas protein to and hybridize to a target motifof the target SCD-associated polynucleotide sequence, and wherein thetarget SCD-associated polynucleotide sequence is cleaved, therebytreating or preventing a disorder associated with expression of theSCD-associated polynucleotide sequence.

In some embodiments, a method for treating or preventing a disorderassociated with expression of a polynucleotide sequence comprises amethod for treating or preventing a disorder associated with expressionof a beta thalassemia-associated polynucleotide sequence.

An exemplary method for treating or preventing a disorder associatedwith expression of a beta thalassemia-associated polynucleotide sequencein a subject comprises (a) altering a target beta thalassemia-associatedpolynucleotide sequence in a cell ex vivo by contacting the betathalassemia-associated polynucleotide sequence with a clusteredregularly interspaced short palindromic repeats-associated (Cas) proteinand from one to two ribonucleic acids, wherein the ribonucleic acidsdirect Cas protein to and hybridize to a target motif of the target betathalassemia-associated polynucleotide sequence, wherein the target betathalassemia-associated polynucleotide sequence is cleaved, and (b)introducing the cell into the subject, thereby treating or preventing adisorder associated with expression of the beta thalassemia-associatedpolynucleotide sequence. In some embodiments of this and other aspects,the efficiency of alteration of cells that express Cas protein is fromabout 50% to about 80%.

An exemplary method for treating or preventing a disorder associatedwith expression of a beta thalassemia-associated polynucleotide sequencein a subject comprises altering a target beta thalassemia-associatedpolynucleotide sequence in a cell by contacting the betathalassemia-associated polynucleotide sequence with a clusteredregularly interspaced short palindromic repeats-associated (Cas) proteinand from one to two ribonucleic acids, wherein the ribonucleic acidsdirect Cas protein to and hybridize to a target motif of the target betathalassemia-associated polynucleotide sequence, and wherein the targetbeta thalassemia-associated polynucleotide sequence is cleaved, therebytreating or preventing a disorder associated with expression of the betathalassemia-associated polynucleotide sequence.

The present invention contemplates altering target polynucleotidesequences in any manner which is available to the skilled artisanutilizing a CRISPR/Cas system of the present invention. Any CRISPR/Cassystem that is capable of altering a target polynucleotide sequence in acell can be used. Such CRISPR-Cas systems can employ a variety of Casproteins (Haft et al. PLoS Comput Biol. 2005; 1(6)e60). The molecularmachinery of such Cas proteins that allows the CRISPR/Cas system toalter target polynucleotide sequences in cells include RNA bindingproteins, endo- and exo-nucleases, helicases, and polymerases. In someembodiments, the CRISPR/Cas system is a CRISPR type I system. In someembodiments, the CRISPR/Cas system is a CRISPR type II system.

The CRISPR/Cas systems of the present invention can be used to alter atarget polynucleotide sequence in a cell. The present inventioncontemplates altering target polynucleotide sequences in a cell for anypurpose. In some embodiments, the target polynucleotide sequence in acell is altered to produce a mutant cell. As used herein, a “mutantcell” refers to a cell with a resulting genotype that differs from itsoriginal genotype. In some instances, a “mutant cell” exhibits a mutantphenotype, for example when a normally functioning gene is altered usingthe CRISPR/Cas systems of the present invention. In other instances, a“mutant cell” exhibits a wild-type phenotype, for example when aCRISPR/Cas system of the present invention is used to correct a mutantgenotype. In exemplary embodiments, a mutant cell exhibits a wild-typeADA phenotype. In exemplary embodiments, a mutant cell exhibits awild-type AK2 phenotype. In exemplary embodiments, a mutant cellexhibits a wild-type CD3D phenotype. In exemplary embodiments, a mutantcell exhibits a wild-type DCLRE1C phenotype. In exemplary embodiments, amutant cell exhibits a wild-type IL2RG phenotype. In exemplaryembodiments, a mutant cell exhibits a wild-type IL7R phenotype. Inexemplary embodiments, a mutant cell exhibits a wild-type JAK3phenotype. In exemplary embodiments, a mutant cell exhibits a wild-typeLIG4 phenotype. In exemplary embodiments, a mutant cell exhibits awild-type NHEJ1 phenotype. In exemplary embodiments, a mutant cellexhibits a wild-type PNP phenotype. In exemplary embodiments, a mutantcell exhibits a wild-type PRKDC phenotype. In exemplary embodiments, amutant cell exhibits a wild-type RAG1 phenotype. In exemplaryembodiments, a mutant cell exhibits a wild-type RAG2 phenotype. Inexemplary embodiments, a mutant cell exhibits a wild-type ZAP70phenotype. In exemplary embodiments, a mutant cell exhibits a wild-typeHBB phenotype. In some embodiments, the target polynucleotide sequencein a cell is altered to correct or repair a genetic mutation (e.g., torestore a normal phenotype to the cell). In an exemplary embodiment, atarget SCID-associated polynucleotide sequence in a cell is altered tocorrect or repair one or more ADA mutations involved in SCID. In anexemplary embodiment, a target SCID-associated polynucleotide sequencein a cell is altered to correct or repair one or more AK2 mutationsinvolved in SCID. In an exemplary embodiment, a target SCID-associatedpolynucleotide sequence in a cell is altered to correct or repair one ormore CD3D mutations involved in SCID. In an exemplary embodiment, atarget SCID-associated polynucleotide sequence in a cell is altered tocorrect or repair one or more DCRE1C mutations involved in SCID. In anexemplary embodiment, a target SCID-associated polynucleotide sequencein a cell is altered to correct or repair one or more IL2RG mutationsinvolved in SCID. In an exemplary embodiment, a target SCID-associatedpolynucleotide sequence in a cell is altered to correct or repair one ormore IL7R mutations involved in SCID. In an exemplary embodiment, atarget SCID-associated polynucleotide sequence in a cell is altered tocorrect or repair one or more JAK3 mutations involved in SCID. In anexemplary embodiment, a target SCID-associated polynucleotide sequencein a cell is altered to correct or repair one or more LIG4 mutationsinvolved in SCID. In an exemplary embodiment, a target SCID-associatedpolynucleotide sequence in a cell is altered to correct or repair one ormore NHEJ1 mutations involved in SCID. In an exemplary embodiment, atarget SCID-associated polynucleotide sequence in a cell is altered tocorrect or repair one or more PNP mutations involved in SCID. In anexemplary embodiment, a target SCID-associated polynucleotide sequencein a cell is altered to correct or repair one or more PRKDC mutationsinvolved in SCID. In an exemplary embodiment, a target SCID-associatedpolynucleotide sequence in a cell is altered to correct or repair one ormore RAG1 mutations involved in SCID. In an exemplary embodiment, atarget SCID-associated polynucleotide sequence in a cell is altered tocorrect or repair one or more RAG2 mutations involved in SCID. In anexemplary embodiment, a target SCID-associated polynucleotide sequencein a cell is altered to correct or repair one or more ZAP70 mutationsinvolved in SCID. In an exemplary embodiment, a target SCD-associatedpolynucleotide sequence in a cell is altered to correct or repair one ormore HBB mutations involved in SCD. In an exemplary embodiment, a targetSCD-associated polynucleotide sequence in a cell is altered to corrector repair one or more HBB mutations involved in SCD. In anotherexemplary embodiment, a target beta thalassemia-associatedpolynucleotide sequence in a cell is altered to correct or repair one ormore HBB mutations involved in beta thalassemia. In some embodiments,the target polynucleotide sequence in a cell is altered to induce agenetic mutation (e.g., to disrupt the function of a gene or genomicelement).

In some embodiments, the alteration is an indel. As used herein, “indel”refers to a mutation resulting from an insertion, deletion, or acombination thereof. As will be appreciated by those skilled in the art,an indel in a coding region of a genomic sequence will result in aframeshift mutation, unless the length of the indel is a multiple ofthree. In some embodiments, the alteration is a point mutation. As usedherein, “point mutation” refers to a substitution that replaces one ofthe nucleotides. A CRISPR/Cas system of the present invention can beused to induce an indel of any length or a point mutation in a targetpolynucleotide sequence.

In some embodiments, the alteration results in a knock out of the targetpolynucleotide sequence or a portion thereof. Knocking out a targetpolynucleotide sequence or a portion thereof using a CRISPR/Cas systemof the present invention can be useful for a variety of applications.For example, knocking out a target polynucleotide sequence in a cell canbe performed in vitro for research purposes. For ex vivo or in vivopurposes, knocking out a target polynucleotide sequence in a cell can beuseful for treating or preventing a disorder associated with expressionof the target polynucleotide sequence.

As used herein, “knock out” includes deleting all or a portion of thetarget polynucleotide sequence in a way that interferes with thefunction of the target polynucleotide sequence. For example, a knock outcan be achieved by altering a target polynucleotide sequence by inducingan indel in the target polynucleotide sequence in a functional domain ofthe target polynucleotide sequence (e.g., a DNA binding domain). Thoseskilled in the art will readily appreciate how to use the CRISPR/Cassystems of the present invention to knock out a target polynucleotidesequence or a portion thereof based upon the details described herein.

In some embodiments, the alteration results in reduced expression of thetarget polynucleotide sequence. The terms “decrease,” “reduced,”“reduction,” and “decrease” are all used herein generally to mean adecrease by a statistically significant amount. However, for avoidanceof doubt, decrease,” “reduced,” “reduction,” “decrease” means a decreaseby at least 10% as compared to a reference level, for example a decreaseby at least about 20%, or at least about 30%, or at least about 40%, orat least about 50%, or at least about 60%, or at least about 70%, or atleast about 80%, or at least about 90% or up to and including a 100%decrease (i.e. absent level as compared to a reference sample), or anydecrease between 10-100% as compared to a reference level.

In some embodiments, the alteration results in increased expression ofthe target polynucleotide sequence. The terms “increased”, “increase” or“enhance” or “activate” are all used herein to generally mean anincrease by a statically significant amount; for the avoidance of anydoubt, the terms “increased”, “increase” or “enhance” or “activate”means an increase of at least 10% as compared to a reference level, forexample an increase of at least about 20%, or at least about 30%, or atleast about 40%, or at least about 50%, or at least about 60%, or atleast about 70%, or at least about 80%, or at least about 90% or up toand including a 100% increase or any increase between 10-100% ascompared to a reference level, or at least about a 2-fold, or at leastabout a 3-fold, or at least about a 4-fold, or at least about a 5-foldor at least about a 10-fold increase, or any increase between 2-fold and10-fold or greater as compared to a reference level.

The term “statistically significant” or “significantly” refers tostatistical significance and generally means a two standard deviation(2SD) below normal, or lower, concentration of the marker. The termrefers to statistical evidence that there is a difference. It is definedas the probability of making a decision to reject the null hypothesiswhen the null hypothesis is actually true. The decision is often madeusing the p-value.

In some embodiments, the alteration is a homozygous alteration. In someembodiments, the alteration is a heterozygous alteration.

In some embodiments, the alteration results in correction of the targetpolynucleotide sequence from an undesired sequence to a desiredsequence. The CRISPR/Cas systems of the present invention can be used tocorrect any type of mutation or error in a target polynucleotidesequence. For example, the CRISPR/Cas systems of the present inventioncan be used to insert a nucleotide sequence that is missing from atarget polynucleotide sequence due to a deletion. The CRISPR/Cas systemsof the present invention can also be used to delete or excise anucleotide sequence from a target polynucleotide sequence due to aninsertion mutation. In some instances, the CRISPR/Cas systems of thepresent invention can be used to replace an incorrect nucleotidesequence with a correct nucleotide sequence (e.g., to restore functionto a target polynucleotide sequence that is impaired due to a loss offunction mutation, i.e., a SNP).

In exemplary embodiments, the CRISPR/Cas systems of the presentinvention can be used to replace mutant ADA polynucleotide sequenceswith wild-type ADA polynucleotide sequences.

In exemplary embodiments, the CRISPR/Cas systems of the presentinvention can be used to replace mutant AK2 polynucleotide sequenceswith wild-type AK2 polynucleotide sequences.

In exemplary embodiments, the CRISPR/Cas systems of the presentinvention can be used to replace mutant CD3D polynucleotide sequenceswith wild-type CD3D polynucleotide sequences.

In exemplary embodiments, the CRISPR/Cas systems of the presentinvention can be used to replace mutant DCLRE1C polynucleotide sequenceswith wild-type DCLRE1C polynucleotide sequences.

In exemplary embodiments, the CRISPR/Cas systems of the presentinvention can be used to replace mutant IL2RG polynucleotide sequenceswith wild-type IL2RG polynucleotide sequences.

In exemplary embodiments, the CRISPR/Cas systems of the presentinvention can be used to replace mutant IL7R polynucleotide sequenceswith wild-type IL7R polynucleotide sequences.

In exemplary embodiments, the CRISPR/Cas systems of the presentinvention can be used to replace mutant JAK3 polynucleotide sequenceswith wild-type JAK3 polynucleotide sequences.

In exemplary embodiments, the CRISPR/Cas systems of the presentinvention can be used to replace mutant LIG4 polynucleotide sequenceswith wild-type LIG4 polynucleotide sequences.

In exemplary embodiments, the CRISPR/Cas systems of the presentinvention can be used to replace mutant NHEJ1 polynucleotide sequenceswith wild-type NHEJ1 polynucleotide sequences.

In exemplary embodiments, the CRISPR/Cas systems of the presentinvention can be used to replace mutant PNP polynucleotide sequenceswith wild-type PNP polynucleotide sequences.

In exemplary embodiments, the CRISPR/Cas systems of the presentinvention can be used to replace mutant PRKDC polynucleotide sequenceswith wild-type PRKDC polynucleotide sequences.

In exemplary embodiments, the CRISPR/Cas systems of the presentinvention can be used to replace mutant RAG1 polynucleotide sequenceswith wild-type RAG1 polynucleotide sequences.

In exemplary embodiments, the CRISPR/Cas systems of the presentinvention can be used to replace mutant RAG2 polynucleotide sequenceswith wild-type RAG2 polynucleotide sequences.

In exemplary embodiments, the CRISPR/Cas systems of the presentinvention can be used to replace mutant ZAP70 polynucleotide sequenceswith wild-type ZAP70 polynucleotide sequences.

In exemplary embodiments, the CRISPR/Cas systems of the presentinvention can be used to replace mutant HBB polynucleotide sequenceswith wild-type HBB polynucleotide sequences.

The CRISPR/Cas systems of the present invention can alter targetpolynucleotides with surprisingly high efficiency as compared toconventional CRISPR/Cas systems. In certain embodiments, the efficiencyof alteration is at least about 5%. In certain embodiments, theefficiency of alteration is at least about 10%. In certain embodiments,the efficiency of alteration is from about 10% to about 80%. In certainembodiments, the efficiency of alteration is from about 30% to about80%. In certain embodiments, the efficiency of alteration is from about50% to about 80%. In some embodiments, the efficiency of alteration isgreater than or equal to about 80%.

The CRISPR/Cas systems of the present invention can be used to alter anytarget polynucleotide sequence in a cell. Those skilled in the art willreadily appreciate that desirable target polynucleotide sequences to bealtered in any particular cell may correspond to any genomic sequencefor which expression of the genomic sequence is associated with adisorder or otherwise facilitates entry of a pathogen into the cell. Forexample, a desirable target polynucleotide sequence to alter in a cellmay be a polynucleotide sequence corresponding to a genomic sequencewhich contains a disease associated single polynucleotide polymorphism(e.g., sickle cell disease, e.g., sickle cell anemia). In such example,the CRISPR/Cas systems of the present invention can be used to correctthe disease associated SNP by replacing it with a wild-type allele(e.g., replacing a Glu6Val SNP in hemoglobin S to Val6Glu, a Glu6Lys SNPin hemoglobin C to Lys6Glu, a Glu121Gln SNP in hemoglobin D toGln121Glu, a Glu121Lys SNP in hemoglobin O to Lys121Glu). As anotherexample, a polynucleotide sequence of a target gene which is responsiblefor entry or proliferation of a pathogen into a cell may be a suitabletarget for deletion or insertion to disrupt the function of the targetgene to prevent the pathogen from entering the cell or proliferatinginside the cell.

In some embodiments, the target polynucleotide sequence is a genomicsequence. In some embodiments, the target polynucleotide sequence is ahuman genomic sequence. In some embodiments, the target polynucleotidesequence is a mammalian genomic sequence. In some embodiments, thetarget polynucleotide sequence is a vertebrate genomic sequence. In someembodiments, the target sequence is a mutant or variant genomic sequence(e.g., a ADA mutant, a AK2 mutant, a CD3D mutant, a DCLRE1C mutant, aIL2RG mutant, a IL7R mutant, a JAK3 mutant, a LIG4 mutant, a NHEJ1mutant, a PNP mutant, a PRKDC mutant, a RAG1 mutant, a RAG2 mutant, aZAP70 mutant, a HBB mutant). In some embodiments, the targetpolynucleotide sequence is a human genomic mutant or variant sequence(e.g., ADA, AK2, CD3D, DCLRE1C, IL2RG, IL7R, JAK3, LIG4, NHEJ1, PNP,PRKDC, RAG1, RAG2, ZAP70, HBB). In some embodiments, the targetpolynucleotide sequence is a mutant or variant mammalian genomicsequence. In some embodiments, the target polynucleotide sequence is amammalian mutant or variant genomic sequence.

In some embodiments, a target polynucleotide sequence is a pathogenicgenomic sequence. Exemplary pathogenic genomic sequences include, butare not limited to a viral genomic sequence, a bacterial genomicsequence, a fungal genomic sequence, a toxin genomic sequence, or aparasitic genomic sequence. In such embodiments, the CRISPR/Cas systemsof the present invention can be used to disrupt the function of apathogen (e.g., to treat or prevent an infection by the pathogen) bycleaving a genomic sequence of the pathogen (e.g., a genomic sequencethat is critical for entry into a cell, or responsible formultiplication, growth or survival once the pathogen is inside a cell).

In some embodiments, the target polynucleotide sequence is anSCID-associated polynucleotide sequence.

In some embodiments, the target polynucleotide sequence is ADA or aportion thereof. In some embodiments, the target polynucleotide sequenceis a variant of ADA or a portion thereof. In some embodiments, thetarget polynucleotide sequence is a homolog of ADA or a portion thereof.In some embodiments, the target polynucleotide sequence is an orthologof ADA or a portion thereof.

In some embodiments, the target polynucleotide sequence is AK2 or aportion thereof. In some embodiments, the target polynucleotide sequenceis a variant of AK2 or a portion thereof. In some embodiments, thetarget polynucleotide sequence is AK2 coding sequence 1 or a portionthereof. In some embodiments, the target polynucleotide sequence is AK2coding sequence 2 or a portion thereof. In some embodiments, the targetpolynucleotide sequence is AK2 coding sequence 3 or a portion thereof.In some embodiments, the target polynucleotide sequence is a homolog ofAK2 or a portion thereof. In some embodiments, the target polynucleotidesequence is an ortholog of AK2 or a portion thereof.

In some embodiments, the target polynucleotide sequence is CD3D or aportion thereof. In some embodiments, the target polynucleotide sequenceis a variant of CD3D or a portion thereof. In some embodiments, thetarget polynucleotide sequence is CD3D coding sequence 1 or a portionthereof. In some embodiments, the target polynucleotide sequence is CD3Dcoding sequence 2 or a portion thereof. In some embodiments, the targetpolynucleotide sequence is a homolog of CD3D or a portion thereof. Insome embodiments, the target polynucleotide sequence is an ortholog ofCD3D or a portion thereof.

In some embodiments, the target polynucleotide sequence is DCLRE1C or aportion thereof. In some embodiments, the target polynucleotide sequenceis a variant of DCLRE1C or a portion thereof. In some embodiments, thetarget polynucleotide sequence is DCLRE1C coding sequence 1 or a portionthereof. In some embodiments, the target polynucleotide sequence isDCLRE1C coding sequence 1 or a portion thereof. In some embodiments, thetarget polynucleotide sequence is DCLRE1C coding sequence 2 or a portionthereof. In some embodiments, the target polynucleotide sequence isDCLRE1C coding sequence 3 or a portion thereof. In some embodiments, thetarget polynucleotide sequence is DCLRE1C coding sequence 4 or a portionthereof. In some embodiments, the target polynucleotide sequence is ahomolog of DCLRE1C or a portion thereof. In some embodiments, the targetpolynucleotide sequence is an ortholog of DCLRE1C or a portion thereof.

In some embodiments, the target polynucleotide sequence is IL2RG or aportion thereof. In some embodiments, the target polynucleotide sequenceis a variant of IL2RG or a portion thereof. In some embodiments, thetarget polynucleotide sequence is a homolog of IL2RG or a portionthereof. In some embodiments, the target polynucleotide sequence is anortholog of IL2RG or a portion thereof.

In some embodiments, the target polynucleotide sequence is IL7R or aportion thereof. In some embodiments, the target polynucleotide sequenceis a variant of IL7R or a portion thereof. In some embodiments, thetarget polynucleotide sequence is a homolog of IL7R or a portionthereof. In some embodiments, the target polynucleotide sequence is anortholog of IL7R or a portion thereof.

In some embodiments, the target polynucleotide sequence is JAK3 or aportion thereof. In some embodiments, the target polynucleotide sequenceis a variant of JAK3 or a portion thereof. In some embodiments, thetarget polynucleotide sequence is a homolog of JAK3 or a portionthereof. In some embodiments, the target polynucleotide sequence is anortholog of JAK3 or a portion thereof.

In some embodiments, the target polynucleotide sequence is LIG4 or aportion thereof. In some embodiments, the target polynucleotide sequenceis a variant of LIG4 or a portion thereof. In some embodiments, thetarget polynucleotide sequence is LIG4 coding sequence 1 or a portionthereof. In some embodiments, the target polynucleotide sequence is LIG4coding sequence 2 or a portion thereof. In some embodiments, the targetpolynucleotide sequence is LIG4 coding sequence 3 or a portion thereof.In some embodiments, the target polynucleotide sequence is a homolog ofLIG4 or a portion thereof. In some embodiments, the targetpolynucleotide sequence is an ortholog of LIG4 or a portion thereof.

In some embodiments, the target polynucleotide sequence is NHEJ1 or aportion thereof. In some embodiments, the target polynucleotide sequenceis a variant of NHEJ1 or a portion thereof. In some embodiments, thetarget polynucleotide sequence is a homolog of NHEJ1 or a portionthereof. In some embodiments, the target polynucleotide sequence is anortholog of NHEJ1 or a portion thereof.

In some embodiments, the target polynucleotide sequence is PNP or aportion thereof. In some embodiments, the target polynucleotide sequenceis a variant of PNP or a portion thereof. In some embodiments, thetarget polynucleotide sequence is a homolog of PNP or a portion thereof.In some embodiments, the target polynucleotide sequence is an orthologof PNP or a portion thereof.

In some embodiments, the target polynucleotide sequence is PRKDC or aportion thereof. In some embodiments, the target polynucleotide sequenceis a variant of PRKDC or a portion thereof. In some embodiments, thetarget polynucleotide sequence is PRKDC coding sequence 1 or a portionthereof. In some embodiments, the target polynucleotide sequence isPRKDC coding sequence 2 or a portion thereof. In some embodiments, thetarget polynucleotide sequence is a homolog of PRKDC or a portionthereof. In some embodiments, the target polynucleotide sequence is anortholog of PRKDC or a portion thereof.

In some embodiments, the target polynucleotide sequence is RAG1 or aportion thereof. In some embodiments, the target polynucleotide sequenceis a variant of RAG1 or a portion thereof. In some embodiments, thetarget polynucleotide sequence is a homolog of RAG1 or a portionthereof. In some embodiments, the target polynucleotide sequence is anortholog of RAG1 or a portion thereof.

In some embodiments, the target polynucleotide sequence is RAG2 or aportion thereof. In some embodiments, the target polynucleotide sequenceis a variant of RAG2 or a portion thereof. In some embodiments, thetarget polynucleotide sequence is RAG2 coding sequence 1 or a portionthereof. In some embodiments, the target polynucleotide sequence is RAG2coding sequence 2 or a portion thereof. In some embodiments, the targetpolynucleotide sequence is RAG2 coding sequence 3 or a portion thereof.In some embodiments, the target polynucleotide sequence is a homolog ofRAG2 or a portion thereof. In some embodiments, the targetpolynucleotide sequence is an ortholog of RAG2 or a portion thereof.

In some embodiments, the target polynucleotide sequence is ZAP70 or aportion thereof. In some embodiments, the target polynucleotide sequenceis a variant of ZAP70 or a portion thereof. In some embodiments, thetarget polynucleotide sequence is ZAP70 coding sequence 1 or a portionthereof. In some embodiments, the target polynucleotide sequence isZAP70 coding sequence 2 or a portion thereof. In some embodiments, thetarget polynucleotide sequence is a homolog of ZAP70 or a portionthereof. In some embodiments, the target polynucleotide sequence is anortholog of ZAP70 or a portion thereof.

In some embodiments, the target polynucleotide sequence is aSCD-associated polynucleotide sequence (e.g., a mutant form of HBB; NCBIGene ID: 3043) or a portion thereof. In some embodiments, the targetpolynucleotide sequence is a mutant homolog of a SCD-associatedpolynucleotide sequence (e.g., a mutated homolog of HBB) or a portionthereof. In some embodiments, the target polynucleotide sequence is amutant ortholog of a SCD-associated polynucleotide sequence (e.g., amutated ortholog of HBB) or a portion thereof.

In some embodiments, the target polynucleotide sequence is a betathalassemia-associated polynucleotide sequence (e.g., a mutant form ofHBB).

In some embodiments, the target polynucleotide sequence is a mutanthomolog of a beta thalassemia-associated polynucleotide sequence (e.g.,a mutated homolog of HBB) or a portion thereof. In some embodiments, thetarget polynucleotide sequence is a mutant ortholog of a betathalassemia-associated polynucleotide sequence (e.g., a mutated orthologof HBB) or a portion thereof. The relevant portions of these targetpolynucleotide sequences correspond to the guide sequences shown inFIGS. 1, 2-4, 5-6, 7-10, 12, 13, 14, 15-17, 18, 19, 20-21, 22, 23-25,26-27, and 11, respectively.

It should be appreciated that the CRISPR/Cas systems of the presentinvention can cleave target polynucleotide sequences in a variety ofways. In some embodiments, the target polynucleotide sequence is cleavedsuch that a double-strand break results. In some embodiments, the targetpolynucleotide sequence is cleaved such that a single-strand breakresults.

The methods of the present invention can be used to alter any targetpolynucleotide sequence in a cell, as long as the target polynucleotidesequence in the cell contains a suitable target motif that allows atleast one ribonucleic acid of the CRISPR/Cas system to direct the Casprotein to and hybridize to the target motif. Those skilled in the artwill appreciate that the target motif for targeting a particularpolynucleotide depends on the CRISPR/Cas system being used, and thesequence of the polynucleotide to be targeted.

In some embodiments, the target motif is at least 20 bp in length. Insome embodiments, the target motif is a 20-nucleotide DNA sequence. Insome embodiments, the target motif is a 20-nucleotide DNA sequencebeginning with G and immediately precedes an NGG motif recognized by theCas protein. In some embodiments, the target motif is G(N)₁₉NGG. In someembodiments, the target motif is a 20-nucleotide DNA sequence andimmediately precedes an NGG motif recognized by the Cas protein. In someembodiments, the target motif is (N)₂₀NGG. It is to be understood thatthe type of target motif for each of the ADA, AK2, CD3D, DCLRE1C, HBB,IL2RG, IL7R, JAK3, LIG4, NHEJ1, PNP, PRKDC, RAG1, RAG2, and ZAP70 targetpolynucleotide sequences can be found in the “site_type” column of FIGS.1, 2-4, 5-6, 7-10, 11, 12, 13, 14, 15-17, 18, 19, 20-21, 22, 23-25, and26-27, respectively.

The target motifs of the present invention can be selected to minimizeoff-target effects of the CRISPR/Cas systems of the present invention.In some embodiments, the target motif is selected such that it containsat least two mismatches when compared with all other genomic nucleotidesequences in the cell. In some embodiments, the target motif is selectedsuch that it contains at least one mismatch when compared with all othergenomic nucleotide sequences in the cell. Those skilled in the art willappreciate that a variety of techniques can be used to select suitabletarget motifs for minimizing off-target effects (e.g., bioinformaticsanalyses).

In some embodiments, the CRISPR/Cas systems of the present inventionutilize homology-directed repair to correct target polynucleotidesequences. In some embodiments, subsequent to cleavage of the targetpolynucleotide sequence, homology-directed repair occurs. In someembodiments, homology-directed repair is performed using an exogenouslyintroduced DNA repair template. The exogenously introduced DNA repairtemplate can be single-stranded or double-stranded. The DNA repairtemplate can be of any length. Those skilled in the art will appreciatethat the length of any particular DNA repair template will depend on thetarget polynucleotide sequence that is to be corrected. The DNA repairtemplate can be designed to repair or replace any target polynucleotidesequence, particularly target polynucleotide sequences comprisingdisease associated polymorphisms (e.g., SNPs). For example,homology-directed repair of a mutant allele comprising such SNPs can beachieved with a CRISPR/Cas system by selecting two target motifs whichflank the mutant allele, and an designing a DNA repair template to matchthe wild-type allele.

In an exemplary embodiment, a cleaved target SCID-associatedpolynucleotide associated sequence is corrected by homology-directedrepair utilizing a corresponding normal wild-type gene sequence as a DNArepair template.

In an exemplary embodiment, a cleaved target SCID-associatedpolynucleotide associated sequence (i.e., mutant ADA) is corrected byhomology-directed repair utilizing a normal wild-type ADA sequence orportions thereof as a DNA repair template.

In an exemplary embodiment, a cleaved target SCID-associatedpolynucleotide associated sequence (i.e., mutant AK2) is corrected byhomology-directed repair utilizing a normal wild-type AK2 sequence(e.g., wild-type AK2 coding sequence 1, AK2 coding sequence 2, and AK2coding sequence 3 or portions thereof) as a DNA repair template.

In an exemplary embodiment, a cleaved target SCID-associatedpolynucleotide associated sequence (i.e., mutant CD3D) is corrected byhomology-directed repair utilizing a normal wild-type CD3D sequence(e.g., wild-type CD3D coding sequence 1, and CD3D coding sequence 2 orportions thereof) as a DNA repair template.

In an exemplary embodiment, a cleaved target SCID-associatedpolynucleotide associated sequence (i.e., mutant DCLRE1C) is correctedby homology-directed repair utilizing a normal wild-type DCLRE1Csequence (e.g., wild-type DCLRE1C coding sequence 1, DCLRE1C codingsequence 2, DCLRE1C coding sequence 3, and DCLRE1C coding sequence 4 orportions thereof) as a DNA repair template.

In an exemplary embodiment, a cleaved target SCID-associatedpolynucleotide associated sequence (i.e., mutant IL2RG) is corrected byhomology-directed repair utilizing a normal wild-type IL2RG sequence orportions thereof as a DNA repair template.

In an exemplary embodiment, a cleaved target SCID-associatedpolynucleotide associated sequence (i.e., mutant IL7R) is corrected byhomology-directed repair utilizing a normal wild-type IL7R sequence orportions thereof as a DNA repair template.

In an exemplary embodiment, a cleaved target SCID-associatedpolynucleotide associated sequence (i.e., mutant JAK3) is corrected byhomology-directed repair utilizing a normal wild-type JAK3 sequence orportions thereof as a DNA repair template.

In an exemplary embodiment, a cleaved target SCID-associatedpolynucleotide associated sequence (i.e., mutant LIG4) is corrected byhomology-directed repair utilizing a normal wild-type LIG4 sequence(e.g., wild-type LIG4 coding sequence 1, LIG4 coding sequence 2, LIG4coding sequence 3, or portions thereof) as a DNA repair template.

In an exemplary embodiment, a cleaved target SCID-associatedpolynucleotide associated sequence (i.e., mutant NHEJ1) is corrected byhomology-directed repair utilizing a normal wild-type NHEJ1 sequence orportions thereof as a DNA repair template.

In an exemplary embodiment, a cleaved target SCID-associatedpolynucleotide associated sequence (i.e., mutant PNP) is corrected byhomology-directed repair utilizing a normal wild-type PNP sequence orportions thereof as a DNA repair template.

In an exemplary embodiment, a cleaved target SCID-associatedpolynucleotide associated sequence (i.e., mutant PRKDC) is corrected byhomology-directed repair utilizing a normal wild-type PRKDC sequence(e.g., wild-type PRKDC coding sequence 1, PRKDC coding sequence 2, orportions thereof) as a DNA repair template.

In an exemplary embodiment, a cleaved target SCID-associatedpolynucleotide associated sequence (i.e., mutant RAG1) is corrected byhomology-directed repair utilizing a normal wild-type RAG1 sequence orportions thereof as a DNA repair template.

In an exemplary embodiment, a cleaved target SCID-associatedpolynucleotide associated sequence (i.e., mutant RAG2) is corrected byhomology-directed repair utilizing a normal wild-type RAG2 sequence(e.g., wild-type RAG2 coding sequence 1, RAG2 coding sequence 2, RAG2coding sequence 3, or portions thereof) as a DNA repair template.

In an exemplary embodiment, a cleaved target SCID-associatedpolynucleotide associated sequence (i.e., mutant ZAP70) is corrected byhomology-directed repair utilizing a normal wild-type ZAP70 sequence(e.g., wild-type ZAP70 coding sequence 1, ZAP70 coding sequence 2, orportions thereof) as a DNA repair template.

In an exemplary embodiment, a cleaved target SCD-associatedpolynucleotide associated sequence is corrected by homology-directedrepair utilizing a normal wild-type HBB sequence or portions thereof asa DNA repair template.

In an exemplary embodiment, a cleaved target beta thalassemia-associatedpolynucleotide associated sequence is corrected by homology-directedrepair utilizing a normal wild-type HBB sequence or portions thereof asa DNA repair template.

In some embodiments, a CRISPR/Cas system of the present inventionincludes a Cas protein and at least one to two one ribonucleic acidsthat are capable of directing the Cas protein to and hybridizing to atarget motif of a target polynucleotide sequence.

As used herein, “protein” and “polypeptide” are used interchangeably torefer to a series of amino acid residues joined by peptide bonds (i.e.,a polymer of amino acids) and include modified amino acids (e.g.,phosphorylated, glycated, glycosolated, etc.) and amino acid analogs.Exemplary polypeptides or proteins include gene products, naturallyoccurring proteins, homologs, paralogs, fragments and other equivalents,variants, and analogs of the above.

In some embodiments, a Cas protein comprises one or more amino acidsubstitutions or modifications. In some embodiments, the one or moreamino acid substitutions comprises a conservative amino acidsubstitution. In some instances, substitutions and/or modifications canprevent or reduce proteolytic degradation and/or extend the half-life ofthe polypeptide in a cell. In some embodiments, the Cas protein cancomprise a peptide bond replacement (e.g., urea, thiourea, carbamate,sulfonyl urea, etc.). In some embodiments, the Cas protein can comprisea naturally occurring amino acid. In some embodiments, the Cas proteincan comprise an alternative amino acid (e.g., D-amino acids, beta-aminoacids, homocysteine, phosphoserine, etc.). In some embodiments, a Casprotein can comprise a modification to include a moiety (e.g.,PEGylation, glycosylation, lipidation, acetylation, end-capping, etc.).

In some embodiments, a Cas protein comprises a core Cas protein.Exemplary Cas core proteins include, but are not limited to Cas1, Cas2,Cas3, Cas4, Cas5, Cas6, Cas7, Cas8 and Cas9. In some embodiments, a Casprotein comprises a Cas protein of an E. coli subtype (also known asCASS2). Exemplary Cas proteins of the E. Coli subtype include, but arenot limited to Cse1, Cse2, Cse3, Cse4, and Cas5e. In some embodiments, aCas protein comprises a Cas protein of the Ypest subtype (also known asCASS3). Exemplary Cas proteins of the Ypest subtype include, but are notlimited to Csy1, Csy2, Csy3, and Csy4. In some embodiments, a Casprotein comprises a Cas protein of the Nmeni subtype (also known asCASS4). Exemplary Cas proteins of the Nmeni subtype include, but are notlimited to Csn1 and Csn2. In some embodiments, a Cas protein comprises aCas protein of the Dvulg subtype (also known as CASS 1). Exemplary Casproteins of the Dvulg subtype include Csd1, Csd2, and Cas5d. In someembodiments, a Cas protein comprises a Cas protein of the Tneap subtype(also known as CASS7). Exemplary Cas proteins of the Tneap subtypeinclude, but are not limited to, Cst1, Cst2, Cas5t. In some embodiments,a Cas protein comprises a Cas protein of the Hmari subtype. ExemplaryCas proteins of the Hmari subtype include, but are not limited to Csh1,Csh2, and Cas5h. In some embodiments, a Cas protein comprises a Casprotein of the Apern subtype (also known as CASS5). Exemplary Casproteins of the Apern subtype include, but are not limited to Csa1,Csa2, Csa3, Csa4, Csa5, and Cas5a. In some embodiments, a Cas proteincomprises a Cas protein of the Mtube subtype (also known as CASS6).Exemplary Cas proteins of the Mtube subtype include, but are not limitedto Csm1, Csm2, Csm3, Csm4, and Csm5. In some embodiments, a Cas proteincomprises a RAMP module Cas protein. Exemplary RAMP module Cas proteinsinclude, but are not limited to, Cmr1, Cmr2, Cmr3, Cmr4, Cmr5, and Cmr6.

In some embodiments, the Cas protein is a Streptococcus pyogenes Cas9protein or a functional portion thereof. In some embodiments, the Casprotein is Cas9 protein from any bacterial species or functional portionthereof. Cas9 protein is a member of the type II CRISPR systems whichtypically include a trans-coded small RNA (tracrRNA), endogenousribonuclease 3 (rnc) and a Cas protein. Cas 9 protein (also known asCRISPR-associated endonuclease Cas9/Csn1) is a polypeptide comprising1368 amino acids. An exemplary amino acid sequence of a Cas9 protein(SEQ ID NO: 298) is shown in FIG. 28. Cas 9 contains 2 enconucleasedomains, including an RuvC-like domain (residues 7-22, 759-766 and982-989) which cleaves target DNA that is noncomplementary to crRNA, andan HNH nuclease domain (residues 810-872) which cleave target DNAcomplementary to crRNA. In FIG. 28, the RuvC-like domain is highlightedin yellow and the HNH nuclease domain is underlined.

As used herein, “functional portion” refers to a portion of a peptidewhich retains its ability to complex with at least one ribonucleic acid(e.g., guide RNA (gRNA)) and cleave a target polynucleotide sequence. Insome embodiments, the functional portion comprises a combination ofoperably linked Cas9 protein functional domains selected from the groupconsisting of a DNA binding domain, at least one RNA binding domain, ahelicase domain, and an endonuclease domain. In some embodiments, thefunctional domains form a complex.

In some embodiments, a functional portion of the Cas9 protein comprisesa functional portion of a RuvC-like domain. In some embodiments, afunctional portion of the Cas9 protein comprises a functional portion ofthe HNH nuclease domain.

It should be appreciated that the present invention contemplates variousof ways of contacting a target polynucleotide sequence with a Casprotein (e.g., Cas9). In some embodiments, exogenous Cas protein can beintroduced into the cell in polypeptide form. In certain embodiments,Cas proteins can be conjugated to or fused to a cell-penetratingpolypeptide or cell-penetrating peptide. As used herein,“cell-penetrating polypeptide” and “cell-penetrating peptide” refers toa polypeptide or peptide, respectively, which facilitates the uptake ofmolecule into a cell. The cell-penetrating polypeptides can contain adetectable label.

In certain embodiments, Cas proteins can be conjugated to or fused to acharged protein (e.g., that carries a positive, negative or overallneutral electric charge). Such linkage may be covalent. In someembodiments, the Cas protein can be fused to a superpositively chargedGFP to significantly increase the ability of the Cas protein topenetrate a cell (Cronican et al. ACS Chem Biol. 2010; 5(8):747-52).

In certain embodiments, the Cas protein can be fused to a proteintransduction domain (PTD) to facilitate its entry into a cell. ExemplaryPTDs include Tat, oligoarginine, and penetratin.

In some embodiments, the Cas9 protein comprises a Cas9 polypeptide fusedto a cell-penetrating peptide. In some embodiments, the Cas9 proteincomprises a Cas9 polypeptide fused to a PTD. In some embodiments, theCas9 protein comprises a Cas9 polypeptide fused to a tat domain. In someembodiments, the Cas9 protein comprises a Cas9 polypeptide fused to anoligoarginine domain. In some embodiments, the Cas9 protein comprises aCas9 polypeptide fused to a penetratin domain. In some embodiments, theCas9 protein comprises a Cas9 polypeptide fused to a superpositivelycharged GFP.

In some embodiments, the Cas protein can be introduced into a cellcontaining the target polynucleotide sequence in the form of a nucleicacid encoding the Cas protein (e.g., Cas9). The process of introducingthe nucleic acids into cells can be achieved by any suitable technique.Suitable techniques include calcium phosphate or lipid-mediatedtransfection, electroporation, and transduction or infection using aviral vector. In some embodiments, the nucleic acid comprises DNA. Insome embodiments, the nucleic acid comprises a modified DNA, asdescribed herein. In some embodiments, the nucleic acid comprises mRNA.In some embodiments, the nucleic acid comprises a modified mRNA, asdescribed herein (e.g., a synthetic, modified mRNA).

In some embodiments, the Cas protein is complexed with the one to tworibonucleic acids. In some embodiments, the Cas protein and the one totwo ribonucleic acids are contained in a nanoparticle. In someembodiments, the Cas protein and the one to two ribonucleic acids arecontained in a lipid nanoparticle, as described herein. In someembodiments, the Cas protein is encoded by a modified nucleic acid, asdescribed herein (e.g., a synthetic, modified mRNA).

The methods of the present invention contemplate the use of anyribonucleic acid that is capable of directing a Cas protein to andhybridizing to a target motif of a target polynucleotide sequence. Insome embodiments, at least one of the ribonucleic acids comprisestracrRNA. In some embodiments, at least one of the ribonucleic acidscomprises CRISPR RNA (crRNA). In some embodiments, at least one of theribonucleic acids comprises a guide RNA that directs the Cas protein toand hybridizes to a target motif of the target polynucleotide sequencein a cell.

The ribonucleic acids of the present invention can be selected tohybridize to a variety of different target motifs, depending on theparticular CRISPR/Cas system employed, and the sequence of the targetpolynucleotide, as will be appreciated by those skilled in the art. Theone to two ribonucleic acids can also be selected to minimizehybridization with nucleic acid sequences other than the targetpolynucleotide sequence. In some embodiments, the one to two ribonucleicacids hybridize to a target motif that contains at least two mismatcheswhen compared with all other genomic nucleotide sequences in the cell.In some embodiments, the one to two ribonucleic acids hybridize to atarget motif that contains at least one mismatch when compared with allother genomic nucleotide sequences in the cell. In some embodiments, theone to two ribonucleic acids are designed to hybridize to a target motifimmediately adjacent to a deoxyribonucleic acid motif recognized by theCas protein. In some embodiments, each of the one to two ribonucleicacids are designed to hybridize to target motifs immediately adjacent todeoxyribonucleic acid motifs recognized by the Cas protein which flank amutant allele located between the target motifs.

In some embodiments, at least one of the one to two ribonucleic acidscomprises a sequence selected from the group consisting of theribonucleic acid sequence of GTAACGGCAGACTTCTCCAC (SEQ ID NO: 5322). Insome embodiments, at least one of the one to two ribonucleic acidscomprises a sequence selected from the group consisting of theribonucleic acid sequence of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321).It should be appreciated that the former sequence is the protospacersequence in the guide RNA, whereas the latter sequence is theprotospacer plus the PAM.

In some embodiments, at least one of the one to two ribonucleic acidscomprises a sequence selected from the group consisting of theribonucleic acid sequences of FIG. 1.

In some embodiments, at least one of the one to two ribonucleic acidscomprises a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of the ribonucleic acid sequences ofFIG. 1.

In some embodiments, at least one of the one to two ribonucleic acidscomprises a sequence selected from the group consisting of theribonucleic acid sequences of FIG. 2. In some embodiments, at least oneof the one to two ribonucleic acids comprises a sequence with a singlenucleotide mismatch to a sequence selected from the group consisting ofthe ribonucleic acid sequences of FIG. 2.

In some embodiments, at least one of the one to two ribonucleic acidscomprises a sequence selected from the group consisting of theribonucleic acid sequences of FIG. 3. In some embodiments, at least oneof the one to two ribonucleic acids comprises a sequence with a singlenucleotide mismatch to a sequence selected from the group consisting ofthe ribonucleic acid sequences of FIG. 3.

In some embodiments, at least one of the one to two ribonucleic acidscomprises a sequence selected from the group consisting of theribonucleic acid sequences of FIG. 4. In some embodiments, at least oneof the one to two ribonucleic acids comprises a sequence with a singlenucleotide mismatch to a sequence selected from the group consisting ofthe ribonucleic acid sequences of FIG. 4.

In some embodiments, at least one of the one to two ribonucleic acidscomprises a sequence selected from the group consisting of theribonucleic acid sequences of FIG. 5. In some embodiments, at least oneof the one to two ribonucleic acids comprises a sequence with a singlenucleotide mismatch to a sequence selected from the group consisting ofthe ribonucleic acid sequences of FIG. 5.

In some embodiments, at least one of the one to two ribonucleic acidscomprises a sequence selected from the group consisting of theribonucleic acid sequences of FIG. 6. In some embodiments, at least oneof the one to two ribonucleic acids comprises a sequence with a singlenucleotide mismatch to a sequence selected from the group consisting ofthe ribonucleic acid sequences of FIG. 6.

In some embodiments, at least one of the one to two ribonucleic acidscomprises a sequence selected from the group consisting of theribonucleic acid sequences of FIG. 7. In some embodiments, at least oneof the one to two ribonucleic acids comprises a sequence with a singlenucleotide mismatch to a sequence selected from the group consisting ofthe ribonucleic acid sequences of FIG. 7.

In some embodiments, at least one of the one to two ribonucleic acidscomprises a sequence selected from the group consisting of theribonucleic acid sequences of FIG. 8. In some embodiments, at least oneof the one to two ribonucleic acids comprises a sequence with a singlenucleotide mismatch to a sequence selected from the group consisting ofthe ribonucleic acid sequences of FIG. 8.

In some embodiments, at least one of the one to two ribonucleic acidscomprises a sequence selected from the group consisting of theribonucleic acid sequences of FIG. 9. In some embodiments, at least oneof the one to two ribonucleic acids comprises a sequence with a singlenucleotide mismatch to a sequence selected from the group consisting ofthe ribonucleic acid sequences of FIG. 9.

In some embodiments, at least one of the one to two ribonucleic acidscomprises a sequence selected from the group consisting of theribonucleic acid sequences of FIG. 10. In some embodiments, at least oneof the one to two ribonucleic acids comprises a sequence with a singlenucleotide mismatch to a sequence selected from the group consisting ofthe ribonucleic acid sequences of FIG. 10.

In some embodiments, at least one of the one to two ribonucleic acidscomprises a sequence selected from the group consisting of theribonucleic acid sequences of FIG. 11. In some embodiments, at least oneof the one to two ribonucleic acids comprises a sequence with a singlenucleotide mismatch to a sequence selected from the group consisting ofthe ribonucleic acid sequences of FIG. 11.

In some embodiments, at least one of the one to two ribonucleic acidscomprises a sequence selected from the group consisting of theribonucleic acid sequences of FIG. 12. In some embodiments, at least oneof the one to two ribonucleic acids comprises a sequence with a singlenucleotide mismatch to a sequence selected from the group consisting ofthe ribonucleic acid sequences of FIG. 12.

In some embodiments, at least one of the one to two ribonucleic acidscomprises a sequence selected from the group consisting of theribonucleic acid sequences of FIG. 13. In some embodiments, at least oneof the one to two ribonucleic acids comprises a sequence with a singlenucleotide mismatch to a sequence selected from the group consisting ofthe ribonucleic acid sequences of FIG. 13.

In some embodiments, at least one of the one to two ribonucleic acidscomprises a sequence selected from the group consisting of theribonucleic acid sequences of FIG. 14. In some embodiments, at least oneof the one to two ribonucleic acids comprises a sequence with a singlenucleotide mismatch to a sequence selected from the group consisting ofthe ribonucleic acid sequences of FIG. 14.

In some embodiments, at least one of the one to two ribonucleic acidscomprises a sequence selected from the group consisting of theribonucleic acid sequences of FIG. 15. In some embodiments, at least oneof the one to two ribonucleic acids comprises a sequence with a singlenucleotide mismatch to a sequence selected from the group consisting ofthe ribonucleic acid sequences of FIG. 15.

In some embodiments, the ribonucleic acid sequences of the at least oneof the one to two ribonucleic acids described above do not include the 3nucleotide NGG sequence. For example, if the target site sequence isGATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleic acid sequenceof the at least one of the one to two ribonucleic acid sequences isGATGCTCAGTACAGCCACCT (SEQ ID NO: 5324). As another example, if thetarget sequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5325), aribonucleic acid sequence with a single nucleotide mismatch which doesnot include the 3 nucleotide NGG sequence is GATGCTGAGTACAGCCACCT (SEQID NO: 5326), with the italicized G being the mismatched nucleotide.Those skilled in the art will appreciate, however, that the singlenucleotide mismatch can comprise any nucleotide in the ribonucleic acid,e.g., the first nucleotide, the second nucleotide, the third nucleotide,the fourth nucleotide, the fifth nucleotide, the sixth nucleotide, theseventh nucleotide, the eighth nucleotide, the ninth nucleotide, thetenth nucleotide, the eleventh nucleotide, the twelfth nucleotide, thethirteenth nucleotide, the fourteenth nucleotide, the fifteenthnucleotide, the sixteenth nucleotide, the seventeenth nucleotide, theeighteenth nucleotide, the nineteenth nucleotide, or the twentiethnucleotide of the ribonucleic acid.

In some embodiments, the ribonucleic acid sequences of the at least oneof the one to two ribonucleic acids described above comprise at least a12 nucleotide fragment of a ribonucleic acid sequence of any of FIGS.1-15. In some embodiments, the ribonucleic acid sequences of the atleast one of the one to two ribonucleic acids described above compriseat least a 12 nucleotide fragment of a sequence with a single nucleotidemismatch to a sequence selected from the group consisting of aribonucleic acid sequence of any of FIGS. 1-15. In some embodiments, theribonucleic acid sequences of the at least one of the one to tworibonucleic acids described above comprise at least a 12 nucleotidefragment of a ribonucleic acid sequence of GTAACGGCAGACTTCTCCACAGG (SEQID NO: 5321). In some embodiments, the ribonucleic acid sequences of theat least one of the one to two ribonucleic acids described abovecomprise at least a 12 nucleotide fragment of a sequence with a singlenucleotide mismatch to a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). For example, if the targetsequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleicacid sequence of the at least one of the one to two ribonucleic acidswhich comprises at least a 12 nucleotide fragment is GTACAGCCACCT (SEQID NO: 5327).

In some embodiments, the ribonucleic acid sequences of the at least oneof the one to two ribonucleic acids described above comprise at least a13 nucleotide fragment of a ribonucleic acid sequence of any of FIGS.1-15. In some embodiments, the ribonucleic acid sequences of the atleast one of the one to two ribonucleic acids described above compriseat least a 13 nucleotide fragment of a sequence with a single nucleotidemismatch to a sequence selected from the group consisting of aribonucleic acid sequence of any of FIGS. 1-15 In some embodiments, theribonucleic acid sequences of the at least one of the one to tworibonucleic acids described above comprise at least a 13 nucleotidefragment of a ribonucleic acid sequence of GTAACGGCAGACTTCTCCACAGG (SEQID NO: 5321). In some embodiments, the ribonucleic acid sequences of theat least one of the one to two ribonucleic acids described abovecomprise at least a 13 nucleotide fragment of a sequence with a singlenucleotide mismatch to a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). For example, if the targetsequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleicacid sequence of the at least one of the one to two ribonucleic acidswhich comprises at least a 13 nucleotide fragment is AGTACAGCCACCT (SEQID NO: 5328).

In some embodiments, the ribonucleic acid sequences of the at least oneof the one to two ribonucleic acids described above comprise at least a14 nucleotide fragment of a ribonucleic acid sequence of any of FIGS.1-15. In some embodiments, the ribonucleic acid sequences of the atleast one of the one to two ribonucleic acids described above compriseat least a 14 nucleotide fragment of a sequence with a single nucleotidemismatch to a sequence selected from the group consisting of aribonucleic acid sequence of any of FIGS. 1-15. In some embodiments, theribonucleic acid sequences of the at least one of the one to tworibonucleic acids described above comprise at least a 14 nucleotidefragment of a ribonucleic acid sequence of GTAACGGCAGACTTCTCCACAGG (SEQID NO: 5321). In some embodiments, the ribonucleic acid sequences of theat least one of the one to two ribonucleic acids described abovecomprise at least a 14 nucleotide fragment of a sequence with a singlenucleotide mismatch to a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). For example, if the targetsequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleicacid sequence of the at least one of the one to two ribonucleic acidswhich comprises at least a 14 nucleotide fragment is CAGTACAGCCACCT (SEQID NO: 5329).

In some embodiments, the ribonucleic acid sequences of the at least oneof the one to two ribonucleic acids described above comprise at least a15 nucleotide fragment of a ribonucleic acid sequence of any of FIGS.1-15. In some embodiments, the ribonucleic acid sequences of the atleast one of the one to two ribonucleic acids described above compriseat least a 15 nucleotide fragment of a sequence with a single nucleotidemismatch to a sequence selected from the group consisting of aribonucleic acid sequence of any of FIGS. 1-15. In some embodiments, theribonucleic acid sequences of the at least one of the one to tworibonucleic acids described above comprise at least a 15 nucleotidefragment of a ribonucleic acid sequence of GTAACGGCAGACTTCTCCACAGG (SEQID NO: 5321). In some embodiments, the ribonucleic acid sequences of theat least one of the one to two ribonucleic acids described abovecomprise at least a 15 nucleotide fragment of a sequence with a singlenucleotide mismatch to a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). For example, if the targetsequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleicacid sequence of the at least one of the one to two ribonucleic acidswhich comprises at least a 15 nucleotide fragment is TCAGTACAGCCACCT(SEQ ID NO: 5330).

In some embodiments, the ribonucleic acid sequences of the at least oneof the one to two ribonucleic acids described above comprise at least a16 nucleotide fragment of a ribonucleic acid sequence of any of FIGS.1-15. In some embodiments, the ribonucleic acid sequences of the atleast one of the one to two ribonucleic acids described above compriseat least a 16 nucleotide fragment of a sequence with a single nucleotidemismatch to a sequence selected from the group consisting of aribonucleic acid sequence of any of FIGS. 1-15. In some embodiments, theribonucleic acid sequences of the at least one of the one to tworibonucleic acids described above comprise at least a 16 nucleotidefragment of a ribonucleic acid sequence of GTAACGGCAGACTTCTCCACAGG (SEQID NO: 5321). In some embodiments, the ribonucleic acid sequences of theat least one of the one to two ribonucleic acids described abovecomprise at least a 16 nucleotide fragment of a sequence with a singlenucleotide mismatch to a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). For example, if the targetsequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleicacid sequence of the at least one of the one to two ribonucleic acidswhich comprises at least a 16 nucleotide fragment is CTCAGTACAGCCACCT(SEQ ID NO: 5331).

In some embodiments, the ribonucleic acid sequences of the at least oneof the one to two ribonucleic acids described above comprise at least a17 nucleotide fragment of a ribonucleic acid sequence of any of FIGS.1-15. In some embodiments, the ribonucleic acid sequences of the atleast one of the one to two ribonucleic acids described above compriseat least a 17 nucleotide fragment of a sequence with a single nucleotidemismatch to a sequence selected from the group consisting of aribonucleic acid sequence of any of FIGS. 1-15. In some embodiments, theribonucleic acid sequences of the at least one of the one to tworibonucleic acids described above comprise at least a 17 nucleotidefragment of a ribonucleic acid sequence of any ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In some embodiments, theribonucleic acid sequences of the at least one of the one to tworibonucleic acids described above comprise at least a 17 nucleotidefragment of a sequence with a single nucleotide mismatch to aribonucleic acid sequence of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321).For example, if the target sequence is GATGCTCAGTACAGCCACCTTGG (SEQ IDNO: 5323), the ribonucleic acid sequence of the at least one of the oneto two ribonucleic acids which comprises at least a 17 nucleotidefragment is GCTCAGTACAGCCACCT (SEQ ID NO: 5332).

In some embodiments, the ribonucleic acid sequences of the at least oneof the one to two ribonucleic acids described above comprise at least a18 nucleotide fragment of a ribonucleic acid sequence of any of FIGS.1-15. In some embodiments, the ribonucleic acid sequences of the atleast one of the one to two ribonucleic acids described above compriseat least a 18 nucleotide fragment of a sequence with a single nucleotidemismatch to a sequence selected from the group consisting of aribonucleic acid sequence of any of FIGS. 1-15. In some embodiments, theribonucleic acid sequences of the at least one of the one to tworibonucleic acids described above comprise at least a 18 nucleotidefragment of a ribonucleic acid sequence of GTAACGGCAGACTTCTCCACAGG (SEQID NO: 5321). In some embodiments, the ribonucleic acid sequences of theat least one of the one to two ribonucleic acids described abovecomprise at least a 18 nucleotide fragment of a sequence with a singlenucleotide mismatch to a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). For example, if the targetsequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleicacid sequence of the at least one of the one to two ribonucleic acidswhich comprises at least a 18 nucleotide fragment is TGCTCAGTACAGCCACCT(SEQ ID NO: 5333).

In some embodiments, the ribonucleic acid sequences of the at least oneof the one to two ribonucleic acids described above comprise at least a19 nucleotide fragment of a ribonucleic acid sequence of any of FIGS.1-15. In some embodiments, the ribonucleic acid sequences of the atleast one of the one to two ribonucleic acids described above compriseat least a 19 nucleotide fragment of a sequence with a single nucleotidemismatch to a sequence selected from the group consisting of aribonucleic acid sequence of any of FIGS. 1-15. In some embodiments, theribonucleic acid sequences of the at least one of the one to tworibonucleic acids described above comprise at least a 19 nucleotidefragment of a ribonucleic acid sequence of GTAACGGCAGACTTCTCCACAGG (SEQID NO: 5321). In some embodiments, the ribonucleic acid sequences of theat least one of the one to two ribonucleic acids described abovecomprise at least a 19 nucleotide fragment of a sequence with a singlenucleotide mismatch to a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). For example, if the targetsequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleicacid sequence of the at least one of the one to two ribonucleic acidswhich comprises at least a 19 nucleotide fragment is ATGCTCAGTACAGCCACCT(SEQ ID NO: 5334).

In some embodiments, the ribonucleic acid sequences of the at least oneof the one to two ribonucleic acids described above comprise at least a20 nucleotide fragment of a ribonucleic acid sequence of any of FIGS.1-15. In some embodiments, the ribonucleic acid sequences of the atleast one of the one to two ribonucleic acids described above compriseat least a 20 nucleotide fragment of a sequence with a single nucleotidemismatch to a sequence selected from the group consisting of aribonucleic acid sequence of any of FIGS. 1-15. In some embodiments, theribonucleic acid sequences of the at least one of the one to tworibonucleic acids described above comprise at least a 20 nucleotidefragment of a ribonucleic acid sequence of GTAACGGCAGACTTCTCCACAGG (SEQID NO: 5321). In some embodiments, the ribonucleic acid sequences of theat least one of the one to two ribonucleic acids described abovecomprise at least a 20 nucleotide fragment of a sequence with a singlenucleotide mismatch to a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). For example, if the targetsequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleicacid sequence of the at least one of the one to two ribonucleic acidswhich comprises at least a 20 nucleotide fragment isGATGCTCAGTACAGCCACCT (SEQ ID NO: 5324).

The present invention also contemplates multiplex genomic editing. Thoseskilled in the art will appreciate that the description above withrespect to genomic editing of a single gene is equally applicable to themultiplex genomic editing embodiments described below.

In another aspect, the present invention provides a method forsimultaneously altering multiple target polynucleotide sequences in acell.

In some embodiments, a method for simultaneously altering multipletarget polynucleotide sequences in a cell comprises a method forsimultaneously altering multiple target SCID-associated polynucleotidesin a cell.

An exemplary method for simultaneously altering multiple targetSCID-associated polynucleotide sequences in a cell comprises contactingthe SCID-associated polynucleotide sequences with a clustered regularlyinterspaced short palindromic repeats-associated (Cas) protein andmultiple ribonucleic acids, wherein the ribonucleic acids direct Casprotein to and hybridize to target motifs of the target SCID-associatedpolynucleotide sequences, wherein the target SCID-associatedpolynucleotide sequences are cleaved. In some embodiments, theefficiency of alteration of cells that express Cas protein is from about50% to about 80%.

In some embodiments, a method for simultaneously altering multipletarget polynucleotide sequences in a cell comprises a method forsimultaneously altering multiple target SCD-associated polynucleotidesin a cell.

An exemplary method for simultaneously altering multiple targetSCD-associated polynucleotide sequences in a cell comprises contactingthe SCD-associated polynucleotide sequences with a clustered regularlyinterspaced short palindromic repeats-associated (Cas) protein andmultiple ribonucleic acids, wherein the ribonucleic acids direct Casprotein to and hybridize to target motifs of the target SCD-associatedpolynucleotide sequences, wherein the target SCD-associatedpolynucleotide sequences are cleaved. In some embodiments, theefficiency of alteration of cells that express Cas protein is from about50% to about 80%.

In some embodiments, a method for simultaneously altering multipletarget polynucleotide sequences in a cell comprises a method forsimultaneously altering multiple target beta thalassemia-associatedpolynucleotides in a cell.

An exemplary method for simultaneously altering multiple target betathalassemia-associated polynucleotide sequences in a cell comprisescontacting the polynucleotide sequences with a clustered regularlyinterspaced short palindromic repeats-associated (Cas) protein andmultiple ribonucleic acids, wherein the ribonucleic acids direct Casprotein to and hybridize to target motifs of the target betathalassemia-associated polynucleotide sequences, wherein the target betathalassemia-associated polynucleotide sequences are cleaved. In someembodiments, the efficiency of alteration of cells that express Casprotein is from about 50% to about 80%.

In yet another aspect, the present invention provides a method fortreating or preventing a disorder associated with expression ofpolynucleotide sequences in a subject.

In some embodiments, a method for treating or preventing a disorderassociated with expression of polynucleotide sequences in a subjectcomprises a method for treating or preventing a disorder associated withexpression of SCID-associated polynucleotide sequences in a subject.

An exemplary method for treating or preventing a disorder associatedwith expression of SCID-associated polynucleotide sequences in a subjectcomprises (a) altering target SCID-associated polynucleotide sequencesin a cell ex vivo by contacting the SCID-associated polynucleotidesequences with a clustered regularly interspaced short palindromicrepeats-associated (Cas) protein and multiple ribonucleic acids, whereinthe ribonucleic acids direct Cas protein to and hybridize to targetmotifs of the target SCID-associated polynucleotide sequences, whereinthe target SCID-associated polynucleotide sequences are cleaved, and (b)introducing the cell into the subject, thereby treating or preventing adisorder associated with expression of the SCID-associatedpolynucleotide sequences. In some embodiments, the efficiency ofalteration of cells that express Cas protein is from about 50% to about80%. In some embodiments, the method includes the step of contacting,before the step of introducing the cell into the subject, the cleavedSCID-associated polynucleotide sequences with an exogenously introducedDNA repair template comprising a corresponding wild-type or normalpolynucleotide sequence, thereby allowing homology-directed repair toreplace the cleaved SCID-associated polynucleotide sequence with thewild-type or normal gene sequence.

In embodiments in which the target SCID-associated polynucleotidesequences comprise ADA polynucleotide sequences, the exogenouslyintroduced DNA repair template comprises a corresponding wild-type ornormal ADA polynucleotide sequence.

In embodiments in which the target SCID-associated polynucleotidesequences comprise AK2 polynucleotide sequences, the exogenouslyintroduced DNA repair template comprises a corresponding wild-type ornormal AK2 polynucleotide sequence.

In embodiments in which the target SCID-associated polynucleotidesequences comprise CD3D polynucleotide sequences, the exogenouslyintroduced DNA repair template comprises a corresponding wild-type ornormal CD3D polynucleotide sequence.

In embodiments in which the target SCID-associated polynucleotidesequences comprise DCLRE1C polynucleotide sequences, the exogenouslyintroduced DNA repair template comprises a corresponding wild-type ornormal DCLRE1C polynucleotide sequence.

In embodiments in which the target SCID-associated polynucleotidesequences comprise IL2RG polynucleotide sequences, the exogenouslyintroduced DNA repair template comprises a corresponding wild-type ornormal IL2RG polynucleotide sequence.

In embodiments in which the target SCID-associated polynucleotidesequences comprise IL7R polynucleotide sequences, the exogenouslyintroduced DNA repair template comprises a corresponding wild-type ornormal IL7R polynucleotide sequence.

In embodiments in which the target SCID-associated polynucleotidesequences comprise JAK3 polynucleotide sequences, the exogenouslyintroduced DNA repair template comprises a corresponding wild-type ornormal JAK3 polynucleotide sequence.

In embodiments in which the target SCID-associated polynucleotidesequences comprise LIG4 polynucleotide sequences, the exogenouslyintroduced DNA repair template comprises a corresponding wild-type ornormal LIG4 polynucleotide sequence.

In embodiments in which the target SCID-associated polynucleotidesequences comprise NHEJ1 polynucleotide sequences, the exogenouslyintroduced DNA repair template comprises a corresponding wild-type ornormal NHEJ1 polynucleotide sequence.

In embodiments in which the target SCID-associated polynucleotidesequences comprise PNP polynucleotide sequences, the exogenouslyintroduced DNA repair template comprises a corresponding wild-type ornormal PNP polynucleotide sequence.

In embodiments in which the target SCID-associated polynucleotidesequences comprise PRKDC polynucleotide sequences, the exogenouslyintroduced DNA repair template comprises a corresponding wild-type ornormal PRKDC polynucleotide sequence.

In embodiments in which the target SCID-associated polynucleotidesequences comprise RAG1 polynucleotide sequences, the exogenouslyintroduced DNA repair template comprises a corresponding wild-type ornormal RAG1 polynucleotide sequence.

In embodiments in which the target SCID-associated polynucleotidesequences comprise RAG2 polynucleotide sequences, the exogenouslyintroduced DNA repair template comprises a corresponding wild-type ornormal RAG2 polynucleotide sequence.

In embodiments in which the target SCID-associated polynucleotidesequences comprise ZAP70 polynucleotide sequences, the exogenouslyintroduced DNA repair template comprises a corresponding wild-type ornormal ZAP70 polynucleotide sequence.

In some embodiments, a method for treating or preventing a disorderassociated with expression of polynucleotide sequences in a subjectcomprises a method for treating or preventing a disorder associated withexpression of SCD-associated polynucleotide sequences in a subject.

An exemplary method for treating or preventing a disorder associatedwith expression of SCD-associated polynucleotide sequences in a subjectcomprises (a) altering target SCD-associated polynucleotide sequences ina cell ex vivo by contacting the SCD-associated polynucleotide sequenceswith a clustered regularly interspaced short palindromicrepeats-associated (Cas) protein and multiple ribonucleic acids, whereinthe ribonucleic acids direct Cas protein to and hybridize to targetmotifs of the target SCD-associated polynucleotide sequences, whereinthe target SCD-associated polynucleotide sequences are cleaved, and (b)introducing the cell into the subject, thereby treating or preventing adisorder associated with expression of the SCD-associated polynucleotidesequences. In some embodiments, the efficiency of alteration of cellsthat express Cas protein is from about 50% to about 80%. In someembodiments, the method includes the step of contacting, before the stepof introducing the cell into the subject, the cleaved SCD-associatedpolynucleotide sequences with an exogenously introduced DNA repairtemplate comprising a normal HBB sequence, thereby allowinghomology-directed repair to replace the cleaved SCD-associatedpolynucleotide sequence with the normal HBB sequence.

In some embodiments, a method for treating or preventing a disorderassociated with expression of polynucleotide sequences in a subjectcomprises a method for treating or preventing a disorder associated withexpression of beta thalassemia-associated polynucleotide sequences in asubject.

An exemplary method for treating or preventing a disorder associatedwith expression of beta thalassemia-associated polynucleotide sequencesin a subject comprises (a) altering target beta thalassemia-associatedpolynucleotide sequences in a cell ex vivo by contacting the betathalassemia-associated polynucleotide sequences with a clusteredregularly interspaced short palindromic repeats-associated (Cas) proteinand multiple ribonucleic acids, wherein the ribonucleic acids direct Casprotein to and hybridize to target motifs of the target betathalassemia-associated polynucleotide sequences, wherein the target betathalassemia-associated polynucleotide sequences are cleaved, and (b)introducing the cell into the subject, thereby treating or preventing adisorder associated with expression of the beta thalassemia-associatedpolynucleotide sequences. In some embodiments, the efficiency ofalteration of cells that express Cas protein is from about 50% to about80%,

In some embodiments, the method includes the step of contacting, beforethe step of introducing the cell into the subject, the cleaved betathalassemia-associated polynucleotide sequences with an exogenouslyintroduced DNA repair template comprising a normal HBB sequence, therebyallowing homology-directed repair to replace the cleaved betathalassemia-associated polynucleotide sequence with the normal HBBsequence.

As used herein, the terms “administering,” “introducing” and“transplanting” are used interchangeably in the context of the placementof cells, e.g. cells described herein comprising a target polynucleotidesequence altered according to the methods of the invention into asubject, by a method or route which results in at least partiallocalization of the introduced cells at a desired site. The cells can beimplanted directly to the desired site, or alternatively be administeredby any appropriate route which results in delivery to a desired locationin the subject where at least a portion of the implanted cells orcomponents of the cells remain viable. The period of viability of thecells after administration to a subject can be as short as a few hours,e.g. twenty-four hours, to a few days, to as long as several years. Insome instances, the cells can also be administered a location other thanthe desired site, such as in the liver or subcutaneously, for example,in a capsule to maintain the implanted cells at the implant location andavoid migration of the implanted cells.

For ex vivo methods, cells can include autologous cells, i.e., a cell orcells taken from a subject who is in need of altering a targetpolynucleotide sequence in the cell or cells (i.e., the donor andrecipient are the same individual). Autologous cells have the advantageof avoiding any immunologically-based rejection of the cells.Alternatively, the cells can be heterologous, e.g., taken from a donor.The second subject can be of the same or different species. Typically,when the cells come from a donor, they will be from a donor who issufficiently immunologically compatible with the recipient, i.e., willnot be subject to transplant rejection, to lessen or remove the need forimmunosuppression. In some embodiments, the cells are taken from axenogeneic source, i.e., a non-human mammal that has been geneticallyengineered to be sufficiently immunologically compatible with therecipient, or the recipient's species. Methods for determiningimmunological compatibility are known in the art, and include tissuetyping to assess donor-recipient compatibility for HLA and ABOdeterminants. See, e.g., Transplantation Immunology, Bach andAuchincloss, Eds. (Wiley, John & Sons, Incorporated 1994).

Any suitable cell culture media can be used for ex vivo methods of theinvention.

Another exemplary method for treating or preventing a disorderassociated with expression of SCID-associated polynucleotide sequencesin a subject comprises altering target SCID-associated polynucleotidesequences in a cell by contacting the SCID-associated polynucleotidesequences with a clustered regularly interspaced short palindromicrepeats-associated (Cas) protein and multiple ribonucleic acids, whereinthe ribonucleic acids direct Cas protein to and hybridize to targetmoieties of the target SCID-associated polynucleotide sequences, andwherein the target SCID-associated polynucleotide sequences are cleaved,thereby treating or preventing a disorder associated with expression ofthe polynucleotide sequences.

In some embodiments, the method includes the step of contacting thecleaved SCID-associated polynucleotide sequences with an exogenouslyintroduced DNA repair template comprising a corresponding wild-type ornormal polynucleotide sequence, thereby allowing homology-directedrepair to replace the cleaved SCID-associated polynucleotide sequencewith the corresponding wild-type or normal polynucleotide sequence.

In embodiments in which the target SCID-associated polynucleotidesequences comprise ADA polynucleotide sequences, the exogenouslyintroduced DNA repair template comprises a corresponding wild-type ornormal ADA polynucleotide sequence.

In embodiments in which the target SCID-associated polynucleotidesequences comprise AK2 polynucleotide sequences, the exogenouslyintroduced DNA repair template comprises a corresponding wild-type ornormal AK2 polynucleotide sequence.

In embodiments in which the target SCID-associated polynucleotidesequences comprise CD3D polynucleotide sequences, the exogenouslyintroduced DNA repair template comprises a corresponding wild-type ornormal CD3D polynucleotide sequence.

In embodiments in which the target SCID-associated polynucleotidesequences comprise DCLRE1C polynucleotide sequences, the exogenouslyintroduced DNA repair template comprises a corresponding wild-type ornormal DCLRE1C polynucleotide sequence.

In embodiments in which the target SCID-associated polynucleotidesequences comprise IL2RG polynucleotide sequences, the exogenouslyintroduced DNA repair template comprises a corresponding wild-type ornormal IL2RG polynucleotide sequence.

In embodiments in which the target SCID-associated polynucleotidesequences comprise IL7R polynucleotide sequences, the exogenouslyintroduced DNA repair template comprises a corresponding wild-type ornormal IL7R polynucleotide sequence.

In embodiments in which the target SCID-associated polynucleotidesequences comprise JAK3 polynucleotide sequences, the exogenouslyintroduced DNA repair template comprises a corresponding wild-type ornormal JAK3 polynucleotide sequence.

In embodiments in which the target SCID-associated polynucleotidesequences comprise LIG4 polynucleotide sequences, the exogenouslyintroduced DNA repair template comprises a corresponding wild-type ornormal LIG4 polynucleotide sequence.

In embodiments in which the target SCID-associated polynucleotidesequences comprise NHEJ1 polynucleotide sequences, the exogenouslyintroduced DNA repair template comprises a corresponding wild-type ornormal NHEJ1 polynucleotide sequence.

In embodiments in which the target SCID-associated polynucleotidesequences comprise PNP polynucleotide sequences, the exogenouslyintroduced DNA repair template comprises a corresponding wild-type ornormal PNP polynucleotide sequence.

In embodiments in which the target SCID-associated polynucleotidesequences comprise PRKDC polynucleotide sequences, the exogenouslyintroduced DNA repair template comprises a corresponding wild-type ornormal PRKDC polynucleotide sequence.

In embodiments in which the target SCID-associated polynucleotidesequences comprise RAG1 polynucleotide sequences, the exogenouslyintroduced DNA repair template comprises a corresponding wild-type ornormal RAG1 polynucleotide sequence.

In embodiments in which the target SCID-associated polynucleotidesequences comprise RAG2 polynucleotide sequences, the exogenouslyintroduced DNA repair template comprises a corresponding wild-type ornormal RAG2 polynucleotide sequence.

In embodiments in which the target SCID-associated polynucleotidesequences comprise ZAP70 polynucleotide sequences, the exogenouslyintroduced DNA repair template comprises a corresponding wild-type ornormal ZAP70 polynucleotide sequence.

Another exemplary method for treating or preventing a disorderassociated with expression of SCD-associated polynucleotide sequences ina subject comprises altering target SCD-associated polynucleotidesequences in a cell by contacting the SCD-associated polynucleotidesequences with a clustered regularly interspaced short palindromicrepeats-associated (Cas) protein and multiple ribonucleic acids, whereinthe ribonucleic acids direct Cas protein to and hybridize to targetmoieties of the target SCD-associated polynucleotide sequences, andwherein the target SCD-associated polynucleotide sequences are cleaved,thereby treating or preventing a disorder associated with expression ofthe polynucleotide sequences.

In some embodiments, the method includes the step of contacting thecleaved SCD-associated polynucleotide sequences with an exogenouslyintroduced DNA repair template comprising a normal HBB sequence, therebyallowing homology-directed repair to replace the cleaved SCD-associatedpolynucleotide sequence with the normal HBB sequence.

Another exemplary method for treating or preventing a disorderassociated with expression of beta thalassemia-associated polynucleotidesequences in a subject comprises altering target betathalassemia-associated polynucleotide sequences in a cell by contactingthe beta thalassemia-associated polynucleotide sequences with aclustered regularly interspaced short palindromic repeats-associated(Cas) protein and multiple ribonucleic acids, wherein the ribonucleicacids direct Cas protein to and hybridize to target moieties of thetarget beta thalassemia-associated polynucleotide sequences, and whereinthe target beta thalassemia-associated polynucleotide sequences arecleaved, thereby treating or preventing a disorder associated withexpression of the beta thalassemia-associated polynucleotide sequences.

In some embodiments, the method includes the step of contacting thecleaved beta thalassemia-associated polynucleotide sequences with anexogenously introduced DNA repair template comprising a normal HBBsequence, thereby allowing homology-directed repair to replace thecleaved beta thalassemia-associated polynucleotide sequence with thenormal HBB sequence.

The terms “subject” and “individual” are used interchangeably herein,and refer to an animal, for example, a human from whom cells can beobtained and/or to whom treatment, including prophylactic treatment,with the cells as described herein, is provided. For treatment of thoseinfections, conditions or disease states which are specific for aspecific animal such as a human subject, the term subject refers to thatspecific animal. The “non-human animals” and “non-human mammals” as usedinterchangeably herein, includes mammals such as rats, mice, rabbits,sheep, cats, dogs, cows, pigs, and non-human primates. The term“subject” also encompasses any vertebrate including but not limited tomammals, reptiles, amphibians and fish. However, advantageously, thesubject is a mammal such as a human, or other mammals such as adomesticated mammal, e.g. dog, cat, horse, and the like, or productionmammal, e.g. cow, sheep, pig, and the like.

In some embodiments, the alteration results in reduced expression of thetarget polynucleotide sequences. In exemplary embodiments, thealteration results in reduced expression of the target SCID-associatedpolynucleotide sequences. In exemplary embodiments, the alterationresults in reduced expression of the target ADA polynucleotidesequences. In exemplary embodiments, the alteration results in reducedexpression of the target AK2 polynucleotide sequences. In exemplaryembodiments, the alteration results in reduced expression of the targetCD3D polynucleotide sequences. In exemplary embodiments, the alterationresults in reduced expression of the target DCLRE1C polynucleotidesequences. In exemplary embodiments, the alteration results in reducedexpression of the target IL2RG polynucleotide sequences. In exemplaryembodiments, the alteration results in reduced expression of the targetIL7R polynucleotide sequences. In exemplary embodiments, the alterationresults in reduced expression of the target JAK3 polynucleotidesequences. In exemplary embodiments, the alteration results in reducedexpression of the target LIG4 polynucleotide sequences. In exemplaryembodiments, the alteration results in reduced expression of the targetNHEJ1 polynucleotide sequences. In exemplary embodiments, the alterationresults in reduced expression of the target PNP polynucleotidesequences. In exemplary embodiments, the alteration results in reducedexpression of the target PRKDC polynucleotide sequences. In exemplaryembodiments, the alteration results in reduced expression of the targetRAG1 polynucleotide sequences. In exemplary embodiments, the alterationresults in reduced expression of the target RAG2 polynucleotidesequences. In exemplary embodiments, the alteration results in reducedexpression of the target ZAP70 polynucleotide sequences. In exemplaryembodiments, the alteration results in reduced expression of the targetSCD-associated polynucleotide sequences. In exemplary embodiments, thealteration results in reduced expression of the target betathalassemia-associated polynucleotide sequences. In some embodiments,the alteration results in a knock out of the target polynucleotidesequences. In exemplary embodiments, the alteration results in a knockout of the target SCID-associated polynucleotide sequences. In exemplaryembodiments, the alteration results in a knock out of the target ADApolynucleotide sequences. In exemplary embodiments, the alterationresults in a knock out of the target AK2 polynucleotide sequences. Inexemplary embodiments, the alteration results in a knock out of thetarget CD3D polynucleotide sequences. In exemplary embodiments, thealteration results in a knock out of the target DCLRE1C polynucleotidesequences. In exemplary embodiments, the alteration results in a knockout of the target IL2RG polynucleotide sequences. In exemplaryembodiments, the alteration results in a knock out of the target IL7Rpolynucleotide sequences. In exemplary embodiments, the alterationresults in a knock out of the target JAK3 polynucleotide sequences. Inexemplary embodiments, the alteration results in a knock out of thetarget LIG4 polynucleotide sequences. In exemplary embodiments, thealteration results in a knock out of the target NHEJ1 polynucleotidesequences. In exemplary embodiments, the alteration results in a knockout of the target PNP polynucleotide sequences. In exemplaryembodiments, the alteration results in a knock out of the target PRKDCpolynucleotide sequences. In exemplary embodiments, the alterationresults in a knock out of the target RAG1 polynucleotide sequences. Inexemplary embodiments, the alteration results in a knock out of thetarget RAG2 polynucleotide sequences. In exemplary embodiments, thealteration results in a knock out of the target ZAP70 polynucleotidesequences. In exemplary embodiments, the alteration results in a knockout of the target SCD-associated polynucleotide sequences. In exemplaryembodiments, the alteration results in a knock out of the target betathalassemia-associated polynucleotide sequences.

In some embodiments, the alteration results in correction of the targetpolynucleotide sequences from undesired sequences to desired sequences.In exemplary embodiments, the alteration results in correction of thetarget SCID-associated polynucleotide sequences to corresponding normalwild-type polynucleotide sequences. In exemplary embodiments, thealteration results in correction of the target SCID-associatedpolynucleotide sequences to corresponding normal wild-type ADAsequences. In exemplary embodiments, the alteration results incorrection of the target SCID-associated polynucleotide sequences tocorresponding normal wild-type AK2 sequences. In exemplary embodiments,the alteration results in correction of the target SCID-associatedpolynucleotide sequences to corresponding normal wild-type CD3Dsequences. In exemplary embodiments, the alteration results incorrection of the target SCID-associated polynucleotide sequences tocorresponding normal wild-type DCLRE1C sequences. In exemplaryembodiments, the alteration results in correction of the targetSCID-associated polynucleotide sequences to corresponding normalwild-type IL2RG sequences In exemplary embodiments, the alterationresults in correction of the target SCID-associated polynucleotidesequences to corresponding normal wild-type IL7R sequences. In exemplaryembodiments, the alteration results in correction of the targetSCID-associated polynucleotide sequences to corresponding normalwild-type JAK3 sequences. In exemplary embodiments, the alterationresults in correction of the target SCID-associated polynucleotidesequences to corresponding normal wild-type LIG4 sequences. In exemplaryembodiments, the alteration results in correction of the targetSCID-associated polynucleotide sequences to corresponding normalwild-type NHEJ1 sequences. In exemplary embodiments, the alterationresults in correction of the target SCID-associated polynucleotidesequences to corresponding normal wild-type PNP sequences. In exemplaryembodiments, the alteration results in correction of the targetSCID-associated polynucleotide sequences to corresponding normalwild-type PRKDC sequences. In exemplary embodiments, the alterationresults in correction of the target SCID-associated polynucleotidesequences to corresponding normal wild-type RAG1 sequences. In exemplaryembodiments, the alteration results in correction of the targetSCID-associated polynucleotide sequences to corresponding normalwild-type RAG2 sequences. In exemplary embodiments, the alterationresults in correction of the target SCID-associated polynucleotidesequences to corresponding normal wild-type ZAP70 sequences. Inexemplary embodiments, the alteration results in correction of thetarget SCD-associated polynucleotide sequences to normal wild-type HBBsequences. In exemplary embodiments, the alteration results incorrection of the target beta thalassemia-associated polynucleotidesequences to normal wild-type HBB sequences. In some embodiments, eachalteration is a homozygous alteration. In some embodiments, theefficiency of alteration at each loci is from about 5% to about 80%. Insome embodiments, the efficiency of alteration at each loci is fromabout 10% to about 80%. In some embodiments, the efficiency ofalteration at each loci is from about 30% to about 80%. In someembodiments, the efficiency of alteration at each loci is from about 50%to about 80%. In some embodiments, the efficiency of alteration at eachloci is from greater than or equal to about 80%.

In some embodiments, each target polynucleotide sequence is cleaved suchthat a double-strand break results. In some embodiments, each targetpolynucleotide sequence is cleaved such that a single-strand breakresults.

In some embodiments, the target polynucleotide sequences comprisemultiple different portions of ADA (e.g., one or more mutations in theADA gene). In some embodiments, the target polynucleotide sequencescomprise at least a portion of ADA.

In some embodiments, the target polynucleotide sequences comprisemultiple different portions of AK2 (e.g., one or more mutations in theAK2 gene). In some embodiments, the target polynucleotide sequencescomprise at least a portion of AK2.

In some embodiments, the target polynucleotide sequences comprisemultiple different portions of CD3D (e.g., one or more mutations in theCD3D gene). In some embodiments, the target polynucleotide sequencescomprise at least a portion of CD3D.

In some embodiments, the target polynucleotide sequences comprisemultiple different portions of DCLRE1C (e.g., one or more mutations inthe DCLRE1C gene). In some embodiments, the target polynucleotidesequences comprise at least a portion of DCLRE1C.

In some embodiments, the target polynucleotide sequences comprisemultiple different portions of IL2RG (e.g., one or more mutations in theIL2RG gene). In some embodiments, the target polynucleotide sequencescomprise at least a portion of IL2RG.

In some embodiments, the target polynucleotide sequences comprisemultiple different portions of IL7R (e.g., one or more mutations in theIL7R gene). In some embodiments, the target polynucleotide sequencescomprise at least a portion of IL7R.

In some embodiments, the target polynucleotide sequences comprisemultiple different portions of JAK3 (e.g., one or more mutations in theJAK3 gene). In some embodiments, the target polynucleotide sequencescomprise at least a portion of JAK3.

In some embodiments, the target polynucleotide sequences comprisemultiple different portions of LIG4 (e.g., one or more mutations in theLIG4 gene). In some embodiments, the target polynucleotide sequencescomprise at least a portion of LIG4.

In some embodiments, the target polynucleotide sequences comprisemultiple different portions of NHEJ1 (e.g., one or more mutations in theNHEJ1 gene). In some embodiments, the target polynucleotide sequencescomprise at least a portion of NHEJ1.

In some embodiments, the target polynucleotide sequences comprisemultiple different portions of PNP (e.g., one or more mutations in thePNP gene). In some embodiments, the target polynucleotide sequencescomprise at least a portion of PNP.

In some embodiments, the target polynucleotide sequences comprisemultiple different portions of PRKDC (e.g., one or more mutations in thePRKDC gene). In some embodiments, the target polynucleotide sequencescomprise at least a portion of PRKDC.

In some embodiments, the target polynucleotide sequences comprisemultiple different portions of RAG1 (e.g., one or more mutations in theRAG1 gene). In some embodiments, the target polynucleotide sequencescomprise at least a portion of RAG1.

In some embodiments, the target polynucleotide sequences comprisemultiple different portions of RAG2 (e.g., one or more mutations in theRAG2 gene). In some embodiments, the target polynucleotide sequencescomprise at least a portion of RAG2.

In some embodiments, the target polynucleotide sequences comprisemultiple different portions of ZAP70 (e.g., one or more mutations in theZAP70 gene). In some embodiments, the target polynucleotide sequencescomprise at least a portion of ZAP70.

In some embodiments, the target polynucleotide sequences comprisemultiple different portions of HBB (e.g., one or more mutations in theHBB gene). In some embodiments, the target polynucleotide sequencescomprise at least a portion of HBB.

In some embodiments, each target motif is a 20-nucleotide DNA sequence.In some embodiments, each target motif is a 20-nucleotide DNA sequencebeginning with G and immediately precedes an NGG motif recognized by theCas protein. In some embodiments, each target motif is a 20-nucleotideDNA sequence and immediately precedes an NGG motif recognized by the Casprotein. In some embodiments, each target motif is G(N)19NGG. In someembodiments, each target motif is (N)20NGG. In some embodiments, eachtarget motif is selected such that it contains at least two mismatcheswhen compared with all other genomic nucleotide sequences in the cell.In some embodiments, each target motif is selected such that it containsat least two mismatches when compared with all other genomic nucleotidesequences in the cell.

In some embodiments, subsequent to cleavage of the target polynucleotidesequences, homology-directed repair occurs. In some embodiments,homology-directed repair is performed using an exogenously introducedDNA repair template. In some embodiments, the exogenously introduced DNArepair template is single-stranded. In some embodiments, the exogenouslyintroduced DNA repair template is double-stranded.

In some embodiments, the exogenously introduced DNA repair template is anormal or wild-type ADA sequence. In some embodiments, the exogenouslyintroduced DNA repair template is a normal or wild-type ADA sequencecorresponding to the mutant ADA sequence comprising the SCID-associatedpolynucleotide sequence.

In some embodiments, the exogenously introduced DNA repair template is anormal or wild-type AK2 sequence. In some embodiments, the exogenouslyintroduced DNA repair template is a normal or wild-type AK2 sequencecorresponding to the mutant AK2 sequence comprising the SCID-associatedpolynucleotide sequence.

In some embodiments, the exogenously introduced DNA repair template is anormal or wild-type CD3D sequence. In some embodiments, the exogenouslyintroduced DNA repair template is a normal or wild-type CD3D sequencecorresponding to the mutant CD3D sequence comprising the SCID-associatedpolynucleotide sequence.

In some embodiments, the exogenously introduced DNA repair template is anormal or wild-type DCLRE1C sequence. In some embodiments, theexogenously introduced DNA repair template is a normal or wild-typeDCLRE1C sequence corresponding to the mutant DCLRE1C sequence comprisingthe SCID-associated polynucleotide sequence.

In some embodiments, the exogenously introduced DNA repair template is anormal or wild-type IL2RG sequence. In some embodiments, the exogenouslyintroduced DNA repair template is a normal or wild-type IL2RG sequencecorresponding to the mutant IL2RG sequence comprising theSCID-associated polynucleotide sequence.

In some embodiments, the exogenously introduced DNA repair template is anormal or wild-type IL7R sequence. In some embodiments, the exogenouslyintroduced DNA repair template is a normal or wild-type IL7R sequencecorresponding to the mutant IL7R sequence comprising the SCID-associatedpolynucleotide sequence.

In some embodiments, the exogenously introduced DNA repair template is anormal or wild-type JAK3 sequence. In some embodiments, the exogenouslyintroduced DNA repair template is a normal or wild-type JAK3 sequencecorresponding to the mutant JAK3 sequence comprising the SCID-associatedpolynucleotide sequence.

In some embodiments, the exogenously introduced DNA repair template is anormal or wild-type LIG4 sequence. In some embodiments, the exogenouslyintroduced DNA repair template is a normal or wild-type LIG4 sequencecorresponding to the mutant LIG4 sequence comprising the SCID-associatedpolynucleotide sequence.

In some embodiments, the exogenously introduced DNA repair template is anormal or wild-type NHEJ1 sequence. In some embodiments, the exogenouslyintroduced DNA repair template is a normal or wild-type NHEJ1 sequencecorresponding to the mutant NHEJ1 sequence comprising theSCID-associated polynucleotide sequence.

In some embodiments, the exogenously introduced DNA repair template is anormal or wild-type PNP sequence. In some embodiments, the exogenouslyintroduced DNA repair template is a normal or wild-type PNP sequencecorresponding to the mutant PNP sequence comprising the SCID-associatedpolynucleotide sequence.

In some embodiments, the exogenously introduced DNA repair template is anormal or wild-type PRKDC sequence. In some embodiments, the exogenouslyintroduced DNA repair template is a normal or wild-type PRKDC sequencecorresponding to the mutant PRKDC sequence comprising theSCID-associated polynucleotide sequence.

In some embodiments, the exogenously introduced DNA repair template is anormal or wild-type RAG1 sequence. In some embodiments, the exogenouslyintroduced DNA repair template is a normal or wild-type RAG1 sequencecorresponding to the mutant RAG1 sequence comprising the SCID-associatedpolynucleotide sequence.

In some embodiments, the exogenously introduced DNA repair template is anormal or wild-type RAG2 sequence. In some embodiments, the exogenouslyintroduced DNA repair template is a normal or wild-type RAG2 sequencecorresponding to the mutant RAG2 sequence comprising the SCID-associatedpolynucleotide sequence.

In some embodiments, the exogenously introduced DNA repair template is anormal or wild-type ZAP70 sequence. In some embodiments, the exogenouslyintroduced DNA repair template is a normal or wild-type ZAP70 sequencecorresponding to the mutant ZAP70 sequence comprising theSCID-associated polynucleotide sequence.

In some embodiments, the exogenously introduced DNA repair template is anormal or wild-type HBB sequence. In some embodiments, the exogenouslyintroduced DNA repair template is a normal or wild-type HBB sequencecorresponding to the mutant HBB sequence comprising the SCD-associatedpolynucleotide sequence. In some embodiments, the exogenously introducedDNA repair template is a normal or wild-type HBB sequence correspondingto the mutant HBB sequence comprising the beta thalassemia-associatedpolynucleotide sequence.

In some embodiments, the Cas protein (e.g., Cas9) is complexed with themultiple ribonucleic acids. In some embodiments, the Cas protein and themultiple ribonucleic acids are contained in nanoparticles, as describedherein. In some embodiments, the Cas protein and the multipleribonucleic acids are contained in lipid nanoparticles, as describedherein. In some embodiments, a nucleic acid encoding a Cas protein andthe multiple ribonucleic acids are contained in nanoparticles. In someembodiments, a nucleic acid encoding a Cas protein and the multipleribonucleic acids are contained in lipid nanoparticles, as describedherein. In some embodiments, a modified, synthetic mRNA encoding a Casprotein as described herein, and multiple ribonucleic acids at least oneof which comprises a modified, synthetic RNA as described herein, arecontained in lipid nanoparticles. In some embodiments, a modified,synthetic mRNA encoding a Cas9 protein as described herein, and multipleribonucleic acids at least one of which comprises a modified, syntheticRNA as described herein, are contained in lipid nanoparticles.

In some embodiments, the multiple ribonucleic acids are selected tominimize hybridization with nucleic acid sequences other than the targetpolynucleotide sequence (e.g., multiple alterations of a single targetpolynucleotide sequence). In some embodiments, the multiple ribonucleicacids are selected to minimize hybridization with nucleic acid sequencesother than the target polynucleotide sequences (e.g., one or morealterations of multiple target polynucleotide sequences). In someembodiments, each of the multiple ribonucleic acids hybridize to targetmotifs that contain at least two mismatches when compared with all othergenomic nucleotide sequences in the cell. In some embodiments, each ofthe multiple ribonucleic acids hybridize to target motifs that containat least one mismatch when compared with all other genomic nucleotidesequences in the cell. In some embodiments, each of the multipleribonucleic acids are designed to hybridize to target motifs immediatelyadjacent to deoxyribonucleic acid motifs recognized by the Cas protein.In some embodiments, each of the multiple ribonucleic acids are designedto hybridize to target motifs immediately adjacent to deoxyribonucleicacid motifs recognized by the Cas protein which flank mutant alleleslocated between the target motifs.

In some embodiments, each of the multiple ribonucleic acids comprises adifferent sequence selected from the group consisting of the ribonucleicacid sequences of FIG. 1. In some embodiments, each of the multipleribonucleic acids comprises a sequence with a single nucleotide mismatchto a different sequence selected from the group consisting of theribonucleic acid sequences of FIG. 1.

In some embodiments, each of the multiple ribonucleic acids comprises adifferent sequence selected from the group consisting of the ribonucleicacid sequences of FIG. 2. In some embodiments, each of the multipleribonucleic acids comprises a sequence with a single nucleotide mismatchto a different sequence selected from the group consisting of theribonucleic acid sequences of FIG. 2.

In some embodiments, each of the multiple ribonucleic acids comprises adifferent sequence selected from the group consisting of the ribonucleicacid sequences of FIG. 3. In some embodiments, each of the multipleribonucleic acids comprises a sequence with a single nucleotide mismatchto a different sequence selected from the group consisting of theribonucleic acid sequences of FIG. 3.

In some embodiments, each of the multiple ribonucleic acids comprises adifferent sequence selected from the group consisting of the ribonucleicacid sequences of FIG. 4. In some embodiments, each of the multipleribonucleic acids comprises a sequence with a single nucleotide mismatchto a different sequence selected from the group consisting of theribonucleic acid sequences of FIG. 4.

In some embodiments, each of the multiple ribonucleic acids comprises adifferent sequence selected from the group consisting of the ribonucleicacid sequences of FIG. 5. In some embodiments, each of the multipleribonucleic acids comprises a sequence with a single nucleotide mismatchto a different sequence selected from the group consisting of theribonucleic acid sequences of FIG. 5.

In some embodiments, each of the multiple ribonucleic acids comprises adifferent sequence selected from the group consisting of the ribonucleicacid sequences of FIG. 6. In some embodiments, each of the multipleribonucleic acids comprises a sequence with a single nucleotide mismatchto a different sequence selected from the group consisting of theribonucleic acid sequences of FIG. 6.

In some embodiments, each of the multiple ribonucleic acids comprises adifferent sequence selected from the group consisting of the ribonucleicacid sequences of FIG. 7. In some embodiments, each of the multipleribonucleic acids comprises a sequence with a single nucleotide mismatchto a different sequence selected from the group consisting of theribonucleic acid sequences of FIG. 7.

In some embodiments, each of the multiple ribonucleic acids comprises adifferent sequence selected from the group consisting of the ribonucleicacid sequences of FIG. 8. In some embodiments, each of the multipleribonucleic acids comprises a sequence with a single nucleotide mismatchto a different sequence selected from the group consisting of theribonucleic acid sequences of FIG. 8.

In some embodiments, each of the multiple ribonucleic acids comprises adifferent sequence selected from the group consisting of the ribonucleicacid sequences of FIG. 9. In some embodiments, each of the multipleribonucleic acids comprises a sequence with a single nucleotide mismatchto a different sequence selected from the group consisting of theribonucleic acid sequences of FIG. 9.

In some embodiments, each of the multiple ribonucleic acids comprises adifferent sequence selected from the group consisting of the ribonucleicacid sequences of FIG. 9. In some embodiments, each of the multipleribonucleic acids comprises a sequence with a single nucleotide mismatchto a different sequence selected from the group consisting of theribonucleic acid sequences of FIG. 9.

In some embodiments, each of the multiple ribonucleic acids comprises adifferent sequence selected from the group consisting of the ribonucleicacid sequences of FIG. 10. In some embodiments, each of the multipleribonucleic acids comprises a sequence with a single nucleotide mismatchto a different sequence selected from the group consisting of theribonucleic acid sequences of FIG. 10.

In some embodiments, each of the multiple ribonucleic acids comprises adifferent sequence selected from the group consisting of the ribonucleicacid sequences of FIG. 11. In some embodiments, each of the multipleribonucleic acids comprises a sequence with a single nucleotide mismatchto a different sequence selected from the group consisting of theribonucleic acid sequences of FIG. 11.

In some embodiments, each of the multiple ribonucleic acids comprises adifferent sequence selected from the group consisting of the ribonucleicacid sequences of FIG. 12. In some embodiments, each of the multipleribonucleic acids comprises a sequence with a single nucleotide mismatchto a different sequence selected from the group consisting of theribonucleic acid sequences of FIG. 12.

In some embodiments, each of the multiple ribonucleic acids comprises adifferent sequence selected from the group consisting of the ribonucleicacid sequences of FIG. 13. In some embodiments, each of the multipleribonucleic acids comprises a sequence with a single nucleotide mismatchto a different sequence selected from the group consisting of theribonucleic acid sequences of FIG. 13.

In some embodiments, each of the multiple ribonucleic acids comprises adifferent sequence selected from the group consisting of the ribonucleicacid sequences of FIG. 14. In some embodiments, each of the multipleribonucleic acids comprises a sequence with a single nucleotide mismatchto a different sequence selected from the group consisting of theribonucleic acid sequences of FIG. 14.

In some embodiments, each of the multiple ribonucleic acids comprises adifferent sequence selected from the group consisting of the ribonucleicacid sequences of FIG. 15. In some embodiments, each of the multipleribonucleic acids comprises a sequence with a single nucleotide mismatchto a different sequence selected from the group consisting of theribonucleic acid sequences of FIG. 15.

In some embodiments, each of the multiple ribonucleic acids comprises adifferent sequence selected from the group consisting of the ribonucleicacid sequences of FIGS. 1-15 and combinations thereof. In someembodiments, the different sequences of the multiple ribonucleic acidsdescribed above do not include the 3 nucleotide NGG sequence.

For example, if a target site sequence is GATGCTCAGTACAGCCACCTTGG (SEQID NO: 5323), a sequence of the multiple ribonucleic acids isGATGCTCAGTACAGCCACCT (SEQ ID NO: 5324). As another example, if thetarget sequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), a sequencewith a single nucleotide mismatch which does not include the 3nucleotide NGG sequence is GATGCTGAGTACAGCCACCT (SEQ ID NO: 5326), withthe italicized G being the mismatched nucleotide. Those skilled in theart will appreciate, however, that the single nucleotide mismatch cancomprise any nucleotide in the ribonucleic acid, e.g., the firstnucleotide, the second nucleotide, the third nucleotide, the fourthnucleotide, the fifth nucleotide, the sixth nucleotide, the seventhnucleotide, the eighth nucleotide, the ninth nucleotide, the tenthnucleotide, the eleventh nucleotide, the twelfth nucleotide, thethirteenth nucleotide, the fourteenth nucleotide, the fifteenthnucleotide, the sixteenth nucleotide, the seventeenth nucleotide, theeighteenth nucleotide, the nineteenth nucleotide, or the twentiethnucleotide of the ribonucleic acid.

In some embodiments, the different sequences of the multiple ribonucleicacids described above comprise at least 12 nucleotide fragments of aribonucleic acid sequence of any of FIGS. 1-15. In some embodiments, thedifferent sequences of the multiple ribonucleic acids described abovecomprise at least 12 nucleotide fragments sequences with singlenucleotide mismatches to a sequence selected from the group consistingof a ribonucleic acid sequence of any of FIGS. 1-15. For example, if atarget sequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), adifferent sequence of the multiple ribonucleic acids comprising at leasta 12 nucleotide fragment with single nucleotide mismatch comprisesGTACAGCCACCT (SEQ ID NO: 5327).

In some embodiments, the different sequences of the multiple ribonucleicacids described above comprise at least 13 nucleotide fragments of aribonucleic acid sequence of any of FIGS. 1-15. In some embodiments, thedifferent sequences of the multiple ribonucleic acids described abovecomprise at least 13 nucleotide fragments sequences with singlenucleotide mismatches to a sequence selected from the group consistingof a ribonucleic acid sequence of any of FIGS. 1-15. For example, if atarget sequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), adifferent sequence of the multiple ribonucleic acids comprising at leasta 13 nucleotide fragment with single nucleotide mismatch comprisesAGTACAGCCACCT (SEQ ID NO: 5328).

In some embodiments, the different sequences of the multiple ribonucleicacids described above comprise at least 14 nucleotide fragments of aribonucleic acid sequence of any of FIGS. 1-15. In some embodiments, thedifferent sequences of the multiple ribonucleic acids described abovecomprise at least 14 nucleotide fragments sequences with singlenucleotide mismatches to a sequence selected from the group consistingof a ribonucleic acid sequence of any of FIGS. 1-15. For example, if atarget sequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), adifferent sequence of the multiple ribonucleic acids comprising at leasta 14 nucleotide fragment with single nucleotide mismatch comprisesCAGTACAGCCACCT (SEQ ID NO: 5329).

In some embodiments, the different sequences of the multiple ribonucleicacids described above comprise at least 15 nucleotide fragments of aribonucleic acid sequence of any of FIGS. 1-15. In some embodiments, thedifferent sequences of the multiple ribonucleic acids described abovecomprise at least 15 nucleotide fragments sequences with singlenucleotide mismatches to a sequence selected from the group consistingof a ribonucleic acid sequence of any of FIGS. 1-15. For example, if atarget sequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), adifferent sequence of the multiple ribonucleic acids comprising at leasta 15 nucleotide fragment with single nucleotide mismatch comprisesTCAGTACAGCCACCT (SEQ ID NO: 5330).

In some embodiments, the different sequences of the multiple ribonucleicacids described above comprise at least 16 nucleotide fragments of aribonucleic acid sequence of any of FIGS. 1-15. In some embodiments, thedifferent sequences of the multiple ribonucleic acids described abovecomprise at least 16 nucleotide fragments sequences with singlenucleotide mismatches to a sequence selected from the group consistingof a ribonucleic acid sequence of any of FIGS. 1-15. For example, if atarget sequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), adifferent sequence of the multiple ribonucleic acids comprising at leasta 16 nucleotide fragment with single nucleotide mismatch comprisesCTCAGTACAGCCACCT (SEQ ID NO: 5331).

In some embodiments, the different sequences of the multiple ribonucleicacids described above comprise at least 17 nucleotide fragments of aribonucleic acid sequence of any of FIGS. 1-15. In some embodiments, thedifferent sequences of the multiple ribonucleic acids described abovecomprise at least 17 nucleotide fragments sequences with singlenucleotide mismatches to a sequence selected from the group consistingof a ribonucleic acid sequence of any of FIGS. 1-15. For example, if atarget sequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), adifferent sequence of the multiple ribonucleic acids comprising at leasta 17 nucleotide fragment with single nucleotide mismatch comprisesGCTCAGTACAGCCACCT (SEQ ID NO: 5332).

In some embodiments, the different sequences of the multiple ribonucleicacids described above comprise at least 18 nucleotide fragments of aribonucleic acid sequence of any of FIGS. 1-15. In some embodiments, thedifferent sequences of the multiple ribonucleic acids described abovecomprise at least 18 nucleotide fragments sequences with singlenucleotide mismatches to a sequence selected from the group consistingof a ribonucleic acid sequence of any of FIGS. 1-15. For example, if atarget sequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), adifferent sequence of the multiple ribonucleic acids comprising at leasta 18 nucleotide fragment with single nucleotide mismatch comprisesTGCTCAGTACAGCCACCT (SEQ ID NO: 5333).

In some embodiments, the different sequences of the multiple ribonucleicacids described above comprise at least 19 nucleotide fragments of aribonucleic acid sequence of any of FIGS. 1-15. In some embodiments, thedifferent sequences of the multiple ribonucleic acids described abovecomprise at least 19 nucleotide fragments sequences with singlenucleotide mismatches to a sequence selected from the group consistingof a ribonucleic acid sequence of any of FIGS. 1-15. For example, if atarget sequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), adifferent sequence of the multiple ribonucleic acids comprising at leasta 19 nucleotide fragment with single nucleotide mismatch comprisesATGCTCAGTACAGCCACCT (SEQ ID NO: 5334).

In some embodiments, the different sequences of the multiple ribonucleicacids described above comprise at least 20 nucleotide fragments of aribonucleic acid sequence of any of FIGS. 1-15. In some embodiments, thedifferent sequences of the multiple ribonucleic acids described abovecomprise at least 20 nucleotide fragments sequences with singlenucleotide mismatches to a sequence selected from the group consistingof a ribonucleic acid sequence of any of FIGS. 1-15. For example, if atarget sequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), adifferent sequence of the multiple ribonucleic acids comprising at leasta 12 nucleotide fragment with single nucleotide mismatch comprisesGATGCTCAGTACAGCCACCT (SEQ ID NO: 5324).

It should be appreciated that any of the Cas protein or the ribonucleicacids can be expressed from a plasmid. In some embodiments, any of theCas protein or the ribonucleic acids are expressed using a promoteroptimized for increased expression in stem cells (e.g., human stemcells). In some embodiments, the promoter is selected from the groupconsisting of a Cytomegalovirus (CMV) early enhancer element and achicken beta-actin promoter, a chicken beta-actin promoter, anelongation factor-1 alpha promoter, and a ubiquitin promoter.

In some embodiments, the methods of the present invention furthercomprise selecting cells that express the Cas protein. The presentinvention contemplates any suitable method for selecting cells. In someembodiments, selecting cells comprises FACS. In some embodiments, FACsis used to select cells which co-express Cas and a fluorescent proteinselected from the group consisting of green fluorescent protein and redfluorescent protein.

The present invention contemplates treating and/or preventing a varietyof disorders which are associated with expression of a targetpolynucleotide sequences. It should be appreciated that the methods andcompositions described herein can be used to treat or prevent disordersassociated with increased expression of a target polynucleotidesequence, as well as decreased expression of a target polynucleotidesequence in a cell. Increased and decreased expression of a targetpolynucleotide sequence includes circumstances where the expressionlevels of the target polynucleotide sequence are increased or decreased,respectively, as well as circumstances in which the function and/orlevel of activity of an expression product of the target polynucleotidesequence increases or decreases, respectively, compared to normalexpression and/or activity levels. Those skilled in the art willappreciate that treating or preventing a disorder associated withincreased expression of a target polynucleotide sequence can be assessedby determining whether the levels and/or activity of the targetpolynucleotide sequence (or an expression product thereof) are decreasedin a relevant cell after employing a method or administering acomposition described herein. The skilled artisan will also appreciatethat treating or preventing a disorder associated with decreasedexpression of a target polynucleotide sequence can be assessed bydetermining whether the levels and/or activity of the targetpolynucleotide sequence (or an expression product thereof) are increasedin the relevant cell after employing a method or administering acomposition described herein.

In some embodiments, the disorder is a genetic disorder. In someembodiments, the disorder is a monogenic disorder. In some embodiments,the disorder is a multigenic disorder. In some embodiments, the disorderis a disorder associated with one or more SNPs. Exemplary disordersassociated with one or more SNPs include a complex disease described inU.S. Pat. No. 7,627,436, Alzheimer's disease as described in PCTInternational Application Publication No. WO/2009/112882, inflammatorydiseases as described in U.S. Patent Application Publication No.2011/0039918, polycystic ovary syndrome as described in U.S. PatentApplication Publication No. 2012/0309642, cardiovascular disease asdescribed in U.S. Pat. No. 7,732,139, Huntington's disease as describedin U.S. Patent Application Publication No. 2012/0136039, thromboembolicdisease as described in European Patent Application Publication No.EP2535424, neurovascular diseases as described in PCT InternationalApplication Publication No. WO/2012/001613, psychosis as described inU.S. Patent Application Publication No. 2010/0292211, multiple sclerosisas described in U.S. Patent Application Publication No. 2011/0319288,schizopherenia, schizoaffective disorder, and bipolar disorder asdescribed in PCT International Application Publication No.WO/2006/023719A2, bipolar disorder and other ailments as described inU.S. Patent Application Publication No. U.S. 2011/0104674, colorectalcancer as described in PCT International Application Publication No.WO/2006/104370A1, a disorder associated with a SNP adjacent to the AKT1gene locus as described in U.S. Patent Application Publication No. U.S.2006/0204969, an eating disorder as described in PCT InternationalApplication Publication No. WO/2003/012143A1, autoimmune disease asdescribed in U.S. Patent Application Publication No. U.S. 2007/0269827,fibrostenosing disease in patients with Chrohn's disease as described inU.S. Pat. No. 7,790,370, and Parkinson's disease as described in U.S.Pat. No. 8,187,811, each of which is incorporated herein by reference inits entirety. Other disorders associated with one or more SNPs which canbe treated or prevented according to the methods of the presentinvention will be apparent to the skilled artisan.

In some embodiments, the disorder is severe combined immunodeficiency.In some embodiments, the disorder is X-linked moderate combinedimmunodeficiency. In some embodiments, the disorder is X-linked severecombined immunodeficiency. In some embodiments, the disorder isadenosine deaminase deficiency or SCID associated with adenosinedeaminase deficiency. In some embodiments, the disorder is Athabascantype SCID. In some embodiments, the disorder is T cell-negative,B-cell/natural killer cell-positive SCID. In some embodiments, thedisorder is T-negative/B-positive type autosomal recessive SCID. In someembodiments, the disorder is SCID with sensitivity to ionizingradiation. In some embodiments, the disorder is SCID with microcephaly,growth retardation, and sensitivity to ionizing radiation. In someembodiments, the disorder is reticular dysgenesis. In some embodiments,the disorder is LIG4 syndrome. In some embodiments, the disorder isalpha/beta T-cell lymphopenia with gamma/delta T-cell expansion, severecytomegalovirus infection, and autoimmunity. In some embodiments, thedisorder is combined cellular and humoral immune defects withgranulomas. In some embodiments, the disorder is B cell-negative SCID.In some embodiments, the disorder is a selective T-cell defect orselective T-cell defect associated with SCID. In some embodiments, thedisorder is purine nucleoside phosphorylase deficiency or SCIDassociated with purine nucleoside phosphorylase deficiency. In someembodiments, the disorder is Omenn syndrome. In some embodiments, thedisorder is bare lymphocyte syndrome. In some embodiments, the disorderis SCID associated with JAK3 mutation. In some embodiments, the disorderis SCID associated with DCLRE1C mutation. In some embodiments, thedisorder is a disorder listed in any one of the Gene PhenotypeRelationship tables listed herein. In some embodiments, the disorder issickle cell anemia. In some embodiments, the disorder is sickle celldisease. In some embodiments, the disorder is sickle cell anemia. Insome embodiments, the disorder is sickle beta thalassemia. In someembodiments, the disorder is beta thalassemia.

The methods of the present invention are capable of altering targetpolynucleotide sequences in a variety of different cells. In someembodiments, the methods of the present invention are used to altertarget polynucleotide sequences in cells ex vivo for subsequentintroduction into a subject. In some embodiments, the methods of thepresent invention can be used to alter target polynucleotide sequencesin cells in vivo. In some embodiments, the cell is a peripheral bloodcell. In some embodiments, the cell is a stem cell or a pluripotentcell. In some embodiments, the cell is a hematopoietic stem cell. Insome embodiments, the cell is a CD34+ cell. In some embodiments, thecell is a CD34+ mobilized peripheral blood cell. In some embodiments,the cell is a CD34+ cord blood cell. In some embodiments, the cell is aCD34+ bone marrow cell. In some embodiments, the cell is aCD34+CD38-Lineage-CD90+CD45RA− cell. In some embodiments, the cell is ahepatocyte. In some embodiments, the cell is a human pluripotent cell.In some embodiments, the cell is a primary human cell. In someembodiments, the cell is a non-transformed cell. In some embodiments,the cell is not a cancer cell. In some embodiments, the cell is not atumor cell. In some embodiments, the cell is not a transformed cell.

In some aspects, the present invention provides a method for altering atarget SCID-associated polynucleotide sequence in a cell comprisingcontacting the SCID-associated polynucleotide sequence in a cellselected from the group consisting of a human pluripotent cell, aprimary human cell, and a non-transformed human cell, with a clusteredregularly interspaced short palindromic repeats-associated (Cas) proteinand from one to two ribonucleic acids, wherein the ribonucleic acidsdirect Cas protein to and hybridize to a target motif of the targetSCID-associated polynucleotide sequence, wherein the targetSCID-associated polynucleotide sequence is cleaved, and wherein theefficiency of alteration of cells that express Cas protein is from about8% to about 80%.

In some aspects, the present invention provides a method for altering atarget SCD-associated polynucleotide sequence in a cell comprisingcontacting the SCD-associated polynucleotide sequence in a cell selectedfrom the group consisting of a human pluripotent cell, a primary humancell, and a non-transformed human cell, with a clustered regularlyinterspaced short palindromic repeats-associated (Cas) protein and fromone to two ribonucleic acids, wherein the ribonucleic acids direct Casprotein to and hybridize to a target motif of the target SCD-associatedpolynucleotide sequence, wherein the target SCD-associatedpolynucleotide sequence is cleaved, and wherein the efficiency ofalteration of cells that express Cas protein is from about 8% to about80%.

In some aspects, the present invention provides a method for altering atarget beta thalassemia-associated polynucleotide sequence in a cellcomprising contacting the beta thalassemia-associated polynucleotidesequence in a cell selected from the group consisting of a humanpluripotent cell, a primary human cell, and a non-transformed humancell, with a clustered regularly interspaced short palindromicrepeats-associated (Cas) protein and from one to two ribonucleic acids,wherein the ribonucleic acids direct Cas protein to and hybridize to atarget motif of the target beta thalassemia-associated polynucleotidesequence, wherein the target beta thalassemia-associated polynucleotidesequence is cleaved, and wherein the efficiency of alteration of cellsthat express Cas protein is from about 8% to about 80%.

In some aspects, the present invention provides a method for treating orpreventing a disorder associated with expression of a SCID-associatedpolynucleotide sequence in a subject, the method comprising (a) alteringa target SCID-associated polynucleotide sequence in a cell ex vivo bycontacting the SCID-associated polynucleotide sequence in a cellselected from the group consisting of a human pluripotent cell, aprimary human cell, and a non-transformed human cell, with a clusteredregularly interspaced short palindromic repeats-associated (Cas) proteinand from one to two ribonucleic acids, wherein the ribonucleic acidsdirect Cas protein to and hybridize to a target motif of the targetSCID-associated polynucleotide sequence, wherein the targetSCID-associated polynucleotide sequence is cleaved, and wherein theefficiency of alteration is from about 8% to about 80%, and (b)introducing the cell into the subject, thereby treating or preventing adisorder associated with expression of the SCID-associatedpolynucleotide sequence.

In some embodiments, the method includes the step of contacting, beforethe step of introducing the cell into the subject, the cleavedSCID-associated polynucleotide sequences with an exogenously introducedDNA repair template comprising a corresponding normal or wild-typepolynucleotide sequence, thereby allowing homology-directed repair toreplace the cleaved SCID-associated polynucleotide sequence with thecorresponding normal or wild type polynucleotide sequence. Inembodiments in which the target SCID-associated polynucleotide sequencescomprise ADA polynucleotide sequences, the exogenously introduced DNArepair template comprises a corresponding wild-type or normal ADApolynucleotide sequence.

In embodiments in which the target SCID-associated polynucleotidesequences comprise AK2 polynucleotide sequences, the exogenouslyintroduced DNA repair template comprises a corresponding wild-type ornormal AK2 polynucleotide sequence.

In embodiments in which the target SCID-associated polynucleotidesequences comprise CD3D polynucleotide sequences, the exogenouslyintroduced DNA repair template comprises a corresponding wild-type ornormal CD3D polynucleotide sequence.

In embodiments in which the target SCID-associated polynucleotidesequences comprise DCLRE1C polynucleotide sequences, the exogenouslyintroduced DNA repair template comprises a corresponding wild-type ornormal DCLRE1C polynucleotide sequence.

In embodiments in which the target SCID-associated polynucleotidesequences comprise IL2RG polynucleotide sequences, the exogenouslyintroduced DNA repair template comprises a corresponding wild-type ornormal IL2RG polynucleotide sequence.

In embodiments in which the target SCID-associated polynucleotidesequences comprise IL7R polynucleotide sequences, the exogenouslyintroduced DNA repair template comprises a corresponding wild-type ornormal IL7R polynucleotide sequence.

In embodiments in which the target SCID-associated polynucleotidesequences comprise JAK3 polynucleotide sequences, the exogenouslyintroduced DNA repair template comprises a corresponding wild-type ornormal JAK3 polynucleotide sequence.

In embodiments in which the target SCID-associated polynucleotidesequences comprise LIG4 polynucleotide sequences, the exogenouslyintroduced DNA repair template comprises a corresponding wild-type ornormal LIG4 polynucleotide sequence.

In embodiments in which the target SCID-associated polynucleotidesequences comprise NHEJ1 polynucleotide sequences, the exogenouslyintroduced DNA repair template comprises a corresponding wild-type ornormal NHEJ1 polynucleotide sequence.

In embodiments in which the target SCID-associated polynucleotidesequences comprise PNP polynucleotide sequences, the exogenouslyintroduced DNA repair template comprises a corresponding wild-type ornormal PNP polynucleotide sequence.

In embodiments in which the target SCID-associated polynucleotidesequences comprise PRKDC polynucleotide sequences, the exogenouslyintroduced DNA repair template comprises a corresponding wild-type ornormal PRKDC polynucleotide sequence.

In embodiments in which the target SCID-associated polynucleotidesequences comprise RAG1 polynucleotide sequences, the exogenouslyintroduced DNA repair template comprises a corresponding wild-type ornormal RAG1 polynucleotide sequence.

In embodiments in which the target SCID-associated polynucleotidesequences comprise RAG2 polynucleotide sequences, the exogenouslyintroduced DNA repair template comprises a corresponding wild-type ornormal RAG2 polynucleotide sequence.

In embodiments in which the target SCID-associated polynucleotidesequences comprise ZAP70 polynucleotide sequences, the exogenouslyintroduced DNA repair template comprises a corresponding wild-type ornormal ZAP70 polynucleotide sequence.

In some aspects, the present invention provides a method for treating orpreventing a disorder associated with expression of a SCD-associatedpolynucleotide sequence in a subject, the method comprising (a) alteringa target SCD-associated polynucleotide sequence in a cell ex vivo bycontacting the SCD-associated polynucleotide sequence in a cell selectedfrom the group consisting of a human pluripotent cell, a primary humancell, and a non-transformed human cell, with a clustered regularlyinterspaced short palindromic repeats-associated (Cas) protein and fromone to two ribonucleic acids, wherein the ribonucleic acids direct Casprotein to and hybridize to a target motif of the target SCD-associatedpolynucleotide sequence, wherein the target SCD-associatedpolynucleotide sequence is cleaved, and wherein the efficiency ofalteration is from about 8% to about 80%, and (b) introducing the cellinto the subject, thereby treating or preventing a disorder associatedwith expression of the SCD-associated polynucleotide sequence.

In some embodiments, the method includes the step of contacting, beforethe step of introducing the cell into the subject, the cleavedSCD-associated polynucleotide sequences with an exogenously introducedDNA repair template comprising a normal HBB sequence, thereby allowinghomology-directed repair to replace the cleaved SCD-associatedpolynucleotide sequence with the normal HBB sequence.

In some aspects, the present invention provides a method for treating orpreventing a disorder associated with expression of a betathalassemia-associated polynucleotide sequence in a subject, the methodcomprising (a) altering a target beta thalassemia-associatedpolynucleotide sequence in a cell ex vivo by contacting the betathalassemia-associated polynucleotide sequence in a cell selected fromthe group consisting of a human pluripotent cell, a primary human cell,and a non-transformed human cell, with a clustered regularly interspacedshort palindromic repeats-associated (Cas) protein and from one to tworibonucleic acids, wherein the ribonucleic acids direct Cas protein toand hybridize to a target motif of the target betathalassemia-associated polynucleotide sequence, wherein the target betathalassemia-associated polynucleotide sequence is cleaved, and whereinthe efficiency of alteration is from about 8% to about 80%, and (b)introducing the cell into the subject, thereby treating or preventing adisorder associated with expression of the beta thalassemia-associatedpolynucleotide sequence.

In some embodiments, the method includes the step of contacting, beforethe step of introducing the cell into the subject, the cleaved betathalassemia-associated polynucleotide sequences with an exogenouslyintroduced DNA repair template comprising a normal HBB sequence, therebyallowing homology-directed repair to replace the cleaved betathalassemia-associated polynucleotide sequence with the normal HBBsequence.

In some aspects, the present invention provides a method forsimultaneously altering multiple target SCID-associated polynucleotidesequences in a cell comprising contacting the SCID-associatedpolynucleotide sequences in a cell selected from the group consisting ofa human pluripotent cell, a primary human cell, and a non-transformedhuman cell, with a clustered regularly interspaced short palindromicrepeats-associated (Cas) protein and multiple ribonucleic acids, whereinthe ribonucleic acids direct Cas protein to and hybridize to targetmotifs of the target SCID-associated polynucleotide sequences, whereinthe target SCD-associated polynucleotide sequences are cleaved, andwherein the efficiency of alteration of cells that express Cas proteinis from about 8% to about 80%.

In some embodiments, the method includes the step of contacting thecleaved target SCID-associated polynucleotide sequences with anexogenously introduced DNA repair template comprising a correspondingnormal or wild-type sequence (e.g., of a ADA gene, a AK2 gene, a CD3Dgene, a DCLRE1C gene, a IL2RG gene, IL7R gene, a LIG4 gene, a NHEJ1gene, a PNP gene, a PRKDC gene, a RAG1 gene, a RAG2 gene, a ZAP70 gene),thereby allowing homology-directed repair to replace the mutant portionof the cleaved SCID-associated polynucleotide sequence with thecorresponding normal or wild-type sequence (e.g., of the ADA gene, theAK2 gene, the CD3D gene, the DCLRE1C gene, the IL2RG gene, the IL7Rgene, the LIG4 gene, the NHEJ1 gene, the PNP gene, the PRKDC gene, theRAG1 gene, the RAG2 gene, the ZAP70 gene).

In some aspects, the present invention provides a method forsimultaneously altering multiple target SCD-associated polynucleotidesequences in a cell comprising contacting the SCD-associatedpolynucleotide sequences in a cell selected from the group consisting ofa human pluripotent cell, a primary human cell, and a non-transformedhuman cell, with a clustered regularly interspaced short palindromicrepeats-associated (Cas) protein and multiple ribonucleic acids, whereinthe ribonucleic acids direct Cas protein to and hybridize to targetmotifs of the target SCD-associated polynucleotide sequences, whereinthe target SCD-associated polynucleotide sequences are cleaved, andwherein the efficiency of alteration of cells that express Cas proteinis from about 8% to about 80%.

In some embodiments, the method includes the step of contacting thecleaved target SCD-associated polynucleotide sequences with anexogenously introduced DNA repair template comprising a normal HBBsequence, thereby allowing homology-directed repair to replace themutant portion of the cleaved SCD-associated polynucleotide sequencewith the normal HBB sequence.

In some aspects, the present invention provides a method forsimultaneously altering multiple target beta thalassemia-associatedpolynucleotide sequences in a cell comprising contacting the betathalassemia-associated polynucleotide sequences in a cell selected fromthe group consisting of a human pluripotent cell, a primary human cell,and a non-transformed human cell, with a clustered regularly interspacedshort palindromic repeats-associated (Cas) protein and multipleribonucleic acids, wherein the ribonucleic acids direct Cas protein toand hybridize to target motifs of the target beta thalassemia-associatedpolynucleotide sequences, wherein the target beta thalassemia-associatedpolynucleotide sequences are cleaved, and wherein the efficiency ofalteration of cells that express Cas protein is from about 8% to about80%.

In some embodiments, the method includes the step of contacting thecleaved target beta thalassemia-associated polynucleotide sequences withan exogenously introduced DNA repair template comprising a normal HBBsequence, thereby allowing homology-directed repair to replace themutant portion of the cleaved beta thalassemia-associated polynucleotidesequence with the normal HBB sequence.

In some aspects, the present invention provides a method for treating orpreventing a disorder associated with expression of SCID-associatedpolynucleotide sequences in a subject, the method comprising (a)altering target SCID-associated polynucleotide sequences in a cell exvivo by contacting the SCD-associated polynucleotide sequences in a cellselected from the group consisting of a human pluripotent cell, aprimary human cell, and a non-transformed human cell, with a clusteredregularly interspaced short palindromic repeats-associated (Cas) proteinand multiple ribonucleic acids, wherein the ribonucleic acids direct Casprotein to and hybridize to target motifs of the target SCID-associatedpolynucleotide sequences, wherein the target SCID-associatedpolynucleotide sequences are cleaved, and wherein the efficiency ofalteration of cells that express Cas protein is from about 8% to about80%, and (b) introducing the cell into the subject, thereby treating orpreventing a disorder associated with expression of the SCID-associatedpolynucleotide sequences.

In some embodiments, the method includes the step of contacting, beforethe step of introducing the cell into the subject, the cleavedSCID-associated polynucleotide sequences with an exogenously introducedDNA repair template comprising a corresponding normal or wild-typesequence (e.g., of a ADA gene, a AK2 gene, a CD3D gene, a DCLRE1C gene,a IL2RG gene, a IL7R gene, a LIG4 gene, a NHEJ1 gene, a PNP gene, aPRKDC gene, a RAG1 gene, a RAG2 gene, a ZAP70 gene), thereby allowinghomology-directed repair to replace the cleaved SCD-associatedpolynucleotide sequence with the normal or wild-type sequence (e.g., ofthe ADA gene, the AK2 gene, the CD3D gene, the DCLRE1C gene, the IL2RGgene, the IL7R gene, the LIG4 gene, the NHEJ1 gene, the PNP gene, thePRKDC gene, the RAG1 gene, the RAG2 gene, the ZAP70 gene).

In some aspects, the present invention provides a method for treating orpreventing a disorder associated with expression of SCD-associatedpolynucleotide sequences in a subject, the method comprising (a)altering target SCD-associated polynucleotide sequences in a cell exvivo by contacting the SCD-associated polynucleotide sequences in a cellselected from the group consisting of a human pluripotent cell, aprimary human cell, and a non-transformed human cell, with a clusteredregularly interspaced short palindromic repeats-associated (Cas) proteinand multiple ribonucleic acids, wherein the ribonucleic acids direct Casprotein to and hybridize to target motifs of the target SCD-associatedpolynucleotide sequences, wherein the target SCD-associatedpolynucleotide sequences are cleaved, and wherein the efficiency ofalteration of cells that express Cas protein is from about 8% to about80%, and (b) introducing the cell into the subject, thereby treating orpreventing a disorder associated with expression of the SCD-associatedpolynucleotide sequences.

In some embodiments, the method includes the step of contacting, beforethe step of introducing the cell into the subject, the cleavedSCD-associated polynucleotide sequences with an exogenously introducedDNA repair template comprising a normal HBB sequence, thereby allowinghomology-directed repair to replace the cleaved SCD-associatedpolynucleotide sequence with the normal HBB sequence.

In some aspects, the present invention provides a method for treating orpreventing a disorder associated with expression of betathalassemia-associated polynucleotide sequences in a subject, the methodcomprising (a) altering target beta thalassemia-associatedpolynucleotide sequences in a cell ex vivo by contacting the betathalassemia-associated polynucleotide sequences in a cell selected fromthe group consisting of a human pluripotent cell, a primary human cell,and a non-transformed human cell, with a clustered regularly interspacedshort palindromic repeats-associated (Cas) protein and multipleribonucleic acids, wherein the ribonucleic acids direct Cas protein toand hybridize to target motifs of the target beta thalassemia-associatedpolynucleotide sequences, wherein the target beta thalassemia-associatedpolynucleotide sequences are cleaved, and wherein the efficiency ofalteration of cells that express Cas protein is from about 8% to about80%, and (b) introducing the cell into the subject, thereby treating orpreventing a disorder associated with expression of the betathalassemia-associated polynucleotide sequences.

In some embodiments, the method includes the step of contacting, beforethe step of introducing the cell into the subject, the cleaved betathalassemia-associated polynucleotide sequences with an exogenouslyintroduced DNA repair template comprising a normal HBB sequence, therebyallowing homology-directed repair to replace the cleaved betathalassemia-associated polynucleotide sequence with the normal HBBsequence.

The present invention also provides compositions comprising Cas proteinsof the present invention or functional portions thereof, nucleic acidsencoding the Cas proteins or functional portions thereof, andribonucleic acid sequences which direct Cas proteins to and hybridize totarget motifs of target polynucleotides in a cell.

For administration to a subject, a composition as disclosed herein canbe administered to a subject, for example in pharmaceutically acceptablecompositions. Pharmaceutically acceptable compositions comprise atherapeutically-effective amount of a Cas protein of the presentinvention or functional portion thereof, nucleic acids encoding the Casproteins (e.g., modified, synthetic mRNA), and ribonucleic acidsequences which direct Cas proteins to and hybridize, formulatedtogether with one or more pharmaceutically acceptable carriers(additives) and/or diluents.

As described in detail below, the pharmaceutical compositions of thepresent invention can be specially formulated for administration insolid or liquid form, including those adapted for the following: (1)oral administration, for example, drenches (aqueous or non-aqueoussolutions or suspensions), lozenges, dragees, capsules, pills, tablets(e.g., those targeted for buccal, sublingual, and systemic absorption),boluses, powders, granules, pastes for application to the tongue; (2)parenteral administration, for example, by subcutaneous, intramuscular,intravenous or epidural injection as, for example, a sterile solution orsuspension, or sustained-release formulation; (3) topical application,for example, as a cream, ointment, or a controlled-release patch orspray applied to the skin; (4) intravaginally or intrarectally, forexample, as a pessary, cream or foam; (5) sublingually; (6) ocularly;(7) transdermally; (8) transmucosally; or (9) nasally. Additionally,compounds can be implanted into a patient or injected using a drugdelivery system. See, for example, Urquhart, et al., Ann. Rev.Pharmacol. Toxicol. 24: 199-236 (1984); Lewis, ed. “Controlled Releaseof Pesticides and Pharmaceuticals” (Plenum Press, New York, 1981); U.S.Pat. No. 3,773,919; and U.S. Pat. No. 35 3,270,960.

As used here, the term “pharmaceutically acceptable” refers to thosecompounds, materials, compositions, and/or dosage forms which are,within the scope of sound medical judgment, suitable for use in contactwith the tissues of human beings and animals without excessive toxicity,irritation, allergic response, or other problem or complication,commensurate with a reasonable benefit/risk ratio.

As used here, the term “pharmaceutically-acceptable carrier” means apharmaceutically-acceptable material, composition or vehicle, such as aliquid or solid filler, diluent, excipient, manufacturing aid (e.g.,lubricant, talc magnesium, calcium or zinc stearate, or steric acid), orsolvent encapsulating material, involved in carrying or transporting thesubject compound from one organ, or portion of the body, to anotherorgan, or portion of the body. Each carrier must be “acceptable” in thesense of being compatible with the other ingredients of the formulationand not injurious to the patient. Some examples of materials which canserve as pharmaceutically-acceptable carriers include: (1) sugars, suchas lactose, glucose and sucrose; (2) starches, such as corn starch andpotato starch; (3) cellulose, and its derivatives, such as sodiumcarboxymethyl cellulose, methylcellulose, ethyl cellulose,microcrystalline cellulose and cellulose acetate; (4) powderedtragacanth; (5) malt; (6) gelatin; (7) lubricating agents, such asmagnesium stearate, sodium lauryl sulfate and talc; (8) excipients, suchas cocoa butter and suppository waxes; (9) oils, such as peanut oil,cottonseed oil, safflower oil, sesame oil, olive oil, corn oil andsoybean oil; (10) glycols, such as propylene glycol; (11) polyols, suchas glycerin, sorbitol, mannitol and polyethylene glycol (PEG); (12)esters, such as ethyl oleate and ethyl laurate; (13) agar; (14)buffering agents, such as magnesium hydroxide and aluminum hydroxide;(15) alginic acid; (16) pyrogen-free water; (17) isotonic saline; (18)Ringer's solution; (19) ethyl alcohol; (20) pH buffered solutions; (21)polyesters, polycarbonates and/or polyanhydrides; (22) bulking agents,such as polypeptides and amino acids (23) serum component, such as serumalbumin, HDL and LDL; (22) C2-C12 alcohols, such as ethanol; and (23)other non-toxic compatible substances employed in pharmaceuticalformulations. Wetting agents, coloring agents, release agents, coatingagents, sweetening agents, flavoring agents, perfuming agents,preservative and antioxidants can also be present in the formulation.The terms such as “excipient”, “carrier”, “pharmaceutically acceptablecarrier” or the like are used interchangeably herein.

The phrase “therapeutically-effective amount” as used herein in respectto a Cas protein and/or ribonucleic acids described herein means thatamount of relevant protein and/or ribonucleic acid, or compositioncomprising the same which is effective for producing some desiredtherapeutic effect in at least a sub-population of cells in an animal ata reasonable benefit/risk ratio applicable to any medical treatment. Forexample, an amount administered to a subject that is sufficient toproduce a statistically significant, measurable change in at least onesymptom of sickle cell anemia (e.g., reduced red blood cell count.).Determination of a therapeutically effective amount is well within thecapability of those skilled in the art. Generally, a therapeuticallyeffective amount can vary with the subject's history, age, condition,sex, as well as the severity and type of the medical condition in thesubject, and administration of other pharmaceutically active agents.

As used herein, the term “administer” refers to the placement of acomposition into a subject by a method or route which results in atleast partial localization of the composition at a desired site suchthat desired effect is produced. A compound or composition describedherein can be administered by any appropriate route known in the artincluding, but not limited to, oral or parenteral routes, includingintravenous, intramuscular, subcutaneous, transdermal, airway (aerosol),pulmonary, nasal, rectal, and topical (including buccal and sublingual)administration.

Exemplary modes of administration include, but are not limited to,injection, infusion, instillation, inhalation, or ingestion. “Injection”includes, without limitation, intravenous, intramuscular, intraarterial,intrathecal, intraventricular, intracapsular, intraorbital,intracardiac, intradermal, intraperitoneal, transtracheal, subcutaneous,subcuticular, intraarticular, sub capsular, subarachnoid, intraspinal,intracerebro spinal, and intrasternal injection and infusion. Inpreferred embodiments, the compositions are administered by intravenousinfusion or injection.

In some aspects, the present invention provides a composition comprisingat least one ribonucleic acid having a sequence selected from the groupconsisting of the ribonucleic acid sequences of FIG. 1.

In some aspects, the present invention provides a composition comprisingat least one ribonucleic acid comprising a sequence with a singlenucleotide mismatch to a sequence selected from the group consisting ofthe ribonucleic acid sequences of FIG. 1.

In some aspects, the present invention provides a composition comprisingat least one ribonucleic acid having a sequence selected from the groupconsisting of the ribonucleic acid sequences of FIG. 2.

In some aspects, the present invention provides a composition comprisingat least one ribonucleic acid comprising a sequence with a singlenucleotide mismatch to a sequence selected from the group consisting ofthe ribonucleic acid sequences of FIG. 2.

In some aspects, the present invention provides a composition comprisingat least one ribonucleic acid having a sequence selected from the groupconsisting of the ribonucleic acid sequences of FIG. 3. In some aspects,the present invention provides a composition comprising at least oneribonucleic acid comprising a sequence with a single nucleotide mismatchto a sequence selected from the group consisting of the ribonucleic acidsequences of FIG. 3.

In some aspects, the present invention provides a composition comprisingat least one ribonucleic acid having a sequence selected from the groupconsisting of the ribonucleic acid sequences of FIG. 4. In some aspects,the present invention provides a composition comprising at least oneribonucleic acid comprising a sequence with a single nucleotide mismatchto a sequence selected from the group consisting of the ribonucleic acidsequences of FIG. 4.

In some aspects, the present invention provides a composition comprisingat least one ribonucleic acid having a sequence selected from the groupconsisting of the ribonucleic acid sequences of FIG. 5. In some aspects,the present invention provides a composition comprising at least oneribonucleic acid comprising a sequence with a single nucleotide mismatchto a sequence selected from the group consisting of the ribonucleic acidsequences of FIG. 5.

In some aspects, the present invention provides a composition comprisingat least one ribonucleic acid having a sequence selected from the groupconsisting of the ribonucleic acid sequences of FIG. 6. In some aspects,the present invention provides a composition comprising at least oneribonucleic acid comprising a sequence with a single nucleotide mismatchto a sequence selected from the group consisting of the ribonucleic acidsequences of FIG. 6.

In some aspects, the present invention provides a composition comprisingat least one ribonucleic acid having a sequence selected from the groupconsisting of the ribonucleic acid sequences of FIG. 7. In some aspects,the present invention provides a composition comprising at least oneribonucleic acid comprising a sequence with a single nucleotide mismatchto a sequence selected from the group consisting of the ribonucleic acidsequences of FIG. 7.

In some aspects, the present invention provides a composition comprisingat least one ribonucleic acid having a sequence selected from the groupconsisting of the ribonucleic acid sequences of FIG. 8. In some aspects,the present invention provides a composition comprising at least oneribonucleic acid comprising a sequence with a single nucleotide mismatchto a sequence selected from the group consisting of the ribonucleic acidsequences of FIG. 8.

In some aspects, the present invention provides a composition comprisingat least one ribonucleic acid having a sequence selected from the groupconsisting of the ribonucleic acid sequences of FIG. 9. In some aspects,the present invention provides a composition comprising at least oneribonucleic acid comprising a sequence with a single nucleotide mismatchto a sequence selected from the group consisting of the ribonucleic acidsequences of FIG. 9.

In some aspects, the present invention provides a composition comprisingat least one ribonucleic acid having a sequence selected from the groupconsisting of the ribonucleic acid sequences of FIG. 10. In someaspects, the present invention provides a composition comprising atleast one ribonucleic acid comprising a sequence with a singlenucleotide mismatch to a sequence selected from the group consisting ofthe ribonucleic acid sequences of FIG. 10.

In some aspects, the present invention provides a composition comprisingat least one ribonucleic acid having a sequence selected from the groupconsisting of the ribonucleic acid sequences of FIG. 11. In someaspects, the present invention provides a composition comprising atleast one ribonucleic acid comprising a sequence with a singlenucleotide mismatch to a sequence selected from the group consisting ofthe ribonucleic acid sequences of FIG. 11.

In some aspects, the present invention provides a composition comprisingat least one ribonucleic acid having a sequence selected from the groupconsisting of the ribonucleic acid sequences of FIG. 12. In someaspects, the present invention provides a composition comprising atleast one ribonucleic acid comprising a sequence with a singlenucleotide mismatch to a sequence selected from the group consisting ofthe ribonucleic acid sequences of FIG. 12.

In some aspects, the present invention provides a composition comprisingat least one ribonucleic acid having a sequence selected from the groupconsisting of the ribonucleic acid sequences of FIG. 13. In someaspects, the present invention provides a composition comprising atleast one ribonucleic acid comprising a sequence with a singlenucleotide mismatch to a sequence selected from the group consisting ofthe ribonucleic acid sequences of FIG. 13.

In some aspects, the present invention provides a composition comprisingat least one ribonucleic acid having a sequence selected from the groupconsisting of the ribonucleic acid sequences of FIG. 14. In someaspects, the present invention provides a composition comprising atleast one ribonucleic acid comprising a sequence with a singlenucleotide mismatch to a sequence selected from the group consisting ofthe ribonucleic acid sequences of FIG. 14.

In some aspects, the present invention provides a composition comprisingat least one ribonucleic acid having a sequence selected from the groupconsisting of the ribonucleic acid sequences of FIG. 15. In someaspects, the present invention provides a composition comprising atleast one ribonucleic acid comprising a sequence with a singlenucleotide mismatch to a sequence selected from the group consisting ofthe ribonucleic acid sequences of FIG. 15.

In some aspects, the present invention provides a composition comprisingat least one ribonucleic acid having a ribonucleic acid sequences ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In some aspects, the presentinvention provides a composition comprising at least one ribonucleicacid comprising a sequence with a single nucleotide mismatch toribonucleic acid sequences of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321).In some embodiments, the at least one ribonucleic acid sequencesdescribed above do not include the 3 nucleotide NGG sequence.

For example, if the target site sequence is GATGCTCAGTACAGCCACCTTGG (SEQID NO: 5323), the ribonucleic acid sequence of the at least oneribonucleic acid sequence is GATGCTCAGTACAGCCACCT (SEQ ID NO: 5324). Asanother example, if the target sequence is GATGCTCAGTACAGCCACCTTGG (SEQID NO: 5323), a ribonucleic acid sequence with a single nucleotidemismatch which does not include the 3 nucleotide NGG sequence isGATGCTGAGTACAGCCACCT (SEQ ID NO: 5326), with the italicized G being themismatched nucleotide. Those skilled in the art will appreciate,however, that the single nucleotide mismatch can comprise any nucleotidein the ribonucleic acid, e.g., the first nucleotide, the secondnucleotide, the third nucleotide, the fourth nucleotide, the fifthnucleotide, the sixth nucleotide, the seventh nucleotide, the eighthnucleotide, the ninth nucleotide, the tenth nucleotide, the eleventhnucleotide, the twelfth nucleotide, the thirteenth nucleotide, thefourteenth nucleotide, the fifteenth nucleotide, the sixteenthnucleotide, the seventeenth nucleotide, the eighteenth nucleotide, thenineteenth nucleotide, or the twentieth nucleotide of the ribonucleicacid.

In some embodiments, the at least one ribonucleic acid described abovecomprises at least a 12 nucleotide fragment of a ribonucleic acidsequence of any of FIGS. 1-15. In some embodiments, the at least oneribonucleic acid described above comprises at least a 12 nucleotidefragment of a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of a ribonucleic acid sequence of anyof FIGS. 1-15. In some embodiments, the at least one ribonucleic aciddescribed above comprises at least a 12 nucleotide fragment of aribonucleic acid sequence of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321).In some embodiments, the at least one ribonucleic acid described abovecomprises at least a 12 nucleotide fragment of a sequence with a singlenucleotide mismatch to a ribonucleic acid sequence of any ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). For example, if the targetsequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleicacid sequence of the at least one ribonucleic acid which comprises atleast a 12 nucleotide fragment is GTACAGCCACCT (SEQ ID NO: 5327).

In some embodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 13 nucleotidefragment of a ribonucleic acid sequence of any of FIGS. 1-15. In someembodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 13 nucleotidefragment of a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of a ribonucleic acid sequence of anyof FIGS. 1-15. In some embodiments, the ribonucleic acid sequence of theat least one ribonucleic acid described above comprises at least a 13nucleotide fragment of a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In some embodiments, theribonucleic acid sequence of the at least one ribonucleic acid describedabove comprises at least a 13 nucleotide fragment of a sequence with asingle nucleotide mismatch to a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). For example, if the targetsequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleicacid sequence of the at least one ribonucleic acid which comprises atleast a 13 nucleotide fragment is AGTACAGCCACCT (SEQ ID NO: 5328).

In some embodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 14 nucleotidefragment of a ribonucleic acid sequence of any of FIGS. 1-15. In someembodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 14 nucleotidefragment of a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of a ribonucleic acid sequence of anyof FIGS. 1-15. In some embodiments, the ribonucleic acid sequence of theat least one ribonucleic acid described above comprises at least a 14nucleotide fragment of a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In some embodiments, theribonucleic acid sequence of the at least one ribonucleic acid describedabove comprises at least a 14 nucleotide fragment of a sequence with asingle nucleotide mismatch to a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). For example, if the targetsequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleicacid sequence of the at least one ribonucleic acid which comprises atleast a 14 nucleotide fragment is CAGTACAGCCACCT (SEQ ID NO: 5329).

In some embodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 15 nucleotidefragment of a ribonucleic acid sequence of any of FIGS. 1-15. In someembodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 15 nucleotidefragment of a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of a ribonucleic acid sequence of anyof FIGS. 1-15. In some embodiments, the ribonucleic acid sequence of theat least one ribonucleic acid described above comprises at least a 15nucleotide fragment of a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In some embodiments, theribonucleic acid sequence of the at least one ribonucleic acid describedabove comprises at least a 15 nucleotide fragment of a sequence with asingle nucleotide mismatch to a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). For example, if the targetsequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleicacid sequence of the at least one ribonucleic acid which comprises atleast a 15 nucleotide fragment is TCAGTACAGCCACCT (SEQ ID NO: 5330).

In some embodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprise at least a 16 nucleotidefragment of a ribonucleic acid sequence of any of FIGS. 1-15. In someembodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 16 nucleotidefragment of a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of a ribonucleic acid sequence of anyof FIGS. 1-15. In some embodiments, the ribonucleic acid sequence of theat least one ribonucleic acid described above comprise at least a 16nucleotide fragment of a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In some embodiments, theribonucleic acid sequence of the at least one ribonucleic acid describedabove comprises at least a 16 nucleotide fragment of a sequence with asingle nucleotide mismatch to a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). For example, if the targetsequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleicacid sequence of the at least one ribonucleic acid which comprises atleast a 16 nucleotide fragment is CTCAGTACAGCCACCT (SEQ ID NO: 5331).

In some embodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 17 nucleotidefragment of a ribonucleic acid sequence of any of FIGS. 1-15. In someembodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 17 nucleotidefragment of a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of a ribonucleic acid sequence of anyof FIGS. 1-15. In some embodiments, the ribonucleic acid sequence of theat least one ribonucleic acid described above comprises at least a 17nucleotide fragment of a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In some embodiments, theribonucleic acid sequence of the at least one ribonucleic acid describedabove comprises at least a 17 nucleotide fragment of a sequence with asingle nucleotide mismatch to a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). For example, if the targetsequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleicacid sequence of the at least one ribonucleic acid which comprises atleast a 17 nucleotide fragment is GCTCAGTACAGCCACCT (SEQ ID NO: 5332).

In some embodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 18 nucleotidefragment of a ribonucleic acid sequence of any of FIGS. 1-15. In someembodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 18 nucleotidefragment of a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of a ribonucleic acid sequence of anyof FIGS. 1-15. In some embodiments, the ribonucleic acid sequence of theat least one ribonucleic acid described above comprises at least a 18nucleotide fragment of a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In some embodiments, theribonucleic acid sequence of the at least one ribonucleic acid describedabove comprises at least a 18 nucleotide fragment of a sequence with asingle nucleotide mismatch to a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). For example, if the targetsequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleicacid sequence of the at least one ribonucleic acid which comprises atleast a 18 nucleotide fragment is TGCTCAGTACAGCCACCT (SEQ ID NO: 5333).

In some embodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprise at least a 19 nucleotidefragment of a ribonucleic acid sequence of any of FIGS. 1-15. In someembodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 19 nucleotidefragment of a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of a ribonucleic acid sequence of anyof FIGS. 1-15. In some embodiments, the ribonucleic acid sequence of theat least one ribonucleic acid described above comprise at least a 19nucleotide fragment of a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In some embodiments, theribonucleic acid sequence of the at least one ribonucleic acid describedabove comprises at least a 19 nucleotide fragment of a sequence with asingle nucleotide mismatch to a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). For example, if the targetsequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleicacid sequence of the at least one ribonucleic acid which comprises atleast a 19 nucleotide fragment is ATGCTCAGTACAGCCACCT (SEQ ID NO: 5334).

In some embodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 20 nucleotidefragment of a ribonucleic acid sequence of any of FIGS. 1-15. In someembodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 20 nucleotidefragment of a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of a ribonucleic acid sequence of anyof FIGS. 1-15. In some embodiments, the ribonucleic acid sequence of theat least one ribonucleic acid described above comprises at least a 20nucleotide fragment of a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In some embodiments, theribonucleic acid sequence of the at least one ribonucleic acid describedabove comprises at least a 20 nucleotide fragment of a sequence with asingle nucleotide mismatch to a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). For example, if the targetsequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleicacid sequence of the at least one ribonucleic acid which comprises atleast a 20 nucleotide fragment is GATGCTCAGTACAGCCACCT (SEQ ID NO:5324).

In some embodiments, the at least one ribonucleic acid in thecomposition is contained in a nanoparticle. In some embodiments, the atleast one ribonucleic acid is contained in a lipid nanoparticle. In someembodiments, the lipid nanoparticle comprises at least one of a cationiclipid, a neutral lipid, an amino lipid, a sterol, and a PEG orPEG-modified lipid.

In some embodiments, at least one of the ribonucleic acids in thecomposition is a modified ribonucleic acid as described herein (e.g., asynthetic, modified ribonucleic acid, e.g., comprising one to twomodified nucleotides selected from the group consisting ofpseudouridine, 5-methylcytodine, 2-thio-uridine,5-methyluridine-5′-triphosphate, 4-thiouridine-5′-triphosphate,5,6-dihydrouridine-5′-triphosphate, and 5-azauridine-5′-triphosphate, orany other modified nucleotides or modifications described herein).

In some embodiments, a composition of the present invention comprises anucleic acid sequence encoding a Cas protein. In some embodiments, acomposition of the present invention comprises nucleic acid sequenceencoding Cas9 protein or a functional portion thereof.

In some embodiments, the nucleic acid encoding the Cas protein (e.g.,Cas9) comprises a modified ribonucleic acid as described herein (e.g., asynthetic, modified mRNA described herein, e.g., comprising at least onemodified nucleotide selected from the group consisting of pseudouridine,5-methylcytodine, 2-thio-uridine, 5-methyluridine-5′-triphosphate,4-thiouridine-5′-triphosphate, 5,6-dihydrouridine-5′-triphosphate, and5-azauridine-5′-triphosphate or any other modified nucleotides ormodifications described herein).

In some aspects, the present invention provides a composition comprisinga chimeric nucleic acid comprising a ribonucleic acid encoding a Casprotein and at least one additional ribonucleic acid having a sequenceselected from the group consisting of the ribonucleic acid sequences ofFIG. 1.

In some aspects, the present invention provides a composition comprisinga chimeric nucleic acid comprising a ribonucleic acid encoding a Casprotein and at least one additional ribonucleic acid having a sequenceselected from the group consisting of the ribonucleic acid sequences ofFIG. 2.

In some aspects, the present invention provides a composition comprisinga chimeric nucleic acid comprising a ribonucleic acid encoding a Casprotein and at least one additional ribonucleic acid having a sequenceselected from the group consisting of the ribonucleic acid sequences ofFIG. 3.

In some aspects, the present invention provides a composition comprisinga chimeric nucleic acid comprising a ribonucleic acid encoding a Casprotein and at least one additional ribonucleic acid having a sequenceselected from the group consisting of the ribonucleic acid sequences ofFIG. 4.

In some aspects, the present invention provides a composition comprisinga chimeric nucleic acid comprising a ribonucleic acid encoding a Casprotein and at least one additional ribonucleic acid having a sequenceselected from the group consisting of the ribonucleic acid sequences ofFIG. 5.

In some aspects, the present invention provides a composition comprisinga chimeric nucleic acid comprising a ribonucleic acid encoding a Casprotein and at least one additional ribonucleic acid having a sequenceselected from the group consisting of the ribonucleic acid sequences ofFIG. 6.

In some aspects, the present invention provides a composition comprisinga chimeric nucleic acid comprising a ribonucleic acid encoding a Casprotein and at least one additional ribonucleic acid having a sequenceselected from the group consisting of the ribonucleic acid sequences ofFIG. 7.

In some aspects, the present invention provides a composition comprisinga chimeric nucleic acid comprising a ribonucleic acid encoding a Casprotein and at least one additional ribonucleic acid having a sequenceselected from the group consisting of the ribonucleic acid sequences ofFIG. 8.

In some aspects, the present invention provides a composition comprisinga chimeric nucleic acid comprising a ribonucleic acid encoding a Casprotein and at least one additional ribonucleic acid having a sequenceselected from the group consisting of the ribonucleic acid sequences ofFIG. 9.

In some aspects, the present invention provides a composition comprisinga chimeric nucleic acid comprising a ribonucleic acid encoding a Casprotein and at least one additional ribonucleic acid having a sequenceselected from the group consisting of the ribonucleic acid sequences ofFIG. 10.

In some aspects, the present invention provides a composition comprisinga chimeric nucleic acid comprising a ribonucleic acid encoding a Casprotein and at least one additional ribonucleic acid having a sequenceselected from the group consisting of the ribonucleic acid sequences ofFIG. 11.

In some aspects, the present invention provides a composition comprisinga chimeric nucleic acid comprising a ribonucleic acid encoding a Casprotein and at least one additional ribonucleic acid having a sequenceselected from the group consisting of the ribonucleic acid sequences ofFIG. 12.

In some aspects, the present invention provides a composition comprisinga chimeric nucleic acid comprising a ribonucleic acid encoding a Casprotein and at least one additional ribonucleic acid having a sequenceselected from the group consisting of the ribonucleic acid sequences ofFIG. 13.

In some aspects, the present invention provides a composition comprisinga chimeric nucleic acid comprising a ribonucleic acid encoding a Casprotein and at least one additional ribonucleic acid having a sequenceselected from the group consisting of the ribonucleic acid sequences ofFIG. 14.

In some aspects, the present invention provides a composition comprisinga chimeric nucleic acid comprising a ribonucleic acid encoding a Casprotein and at least one additional ribonucleic acid having a sequenceselected from the group consisting of the ribonucleic acid sequences ofFIG. 15.

In some aspects, the present invention provides a composition comprisinga chimeric nucleic acid comprising a ribonucleic acid encoding a Casprotein and at least one additional ribonucleic acid having aribonucleic acid sequence of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321).

In some embodiments, the at least one additional ribonucleic acidsequences described above do not include the 3 nucleotide NGG sequence.

For example, if the target site sequence is GATGCTCAGTACAGCCACCTTGG (SEQID NO: 5323), the ribonucleic acid sequence of the at least oneadditional ribonucleic acid is GATGCTCAGTACAGCCACCT (SEQ ID NO: 5324).As another example, if the target sequence is GATGCTCAGTACAGCCACCTTGG(SEQ ID NO: 5323), a ribonucleic acid sequence with a single nucleotidemismatch which does not include the 3 nucleotide NGG sequence isGATGCTGAGTACAGCCACCT (SEQ ID NO: 5326), with the italicized G being themismatched nucleotide. Those skilled in the art will appreciate,however, that the single nucleotide mismatch can comprise any nucleotidein the ribonucleic acid, e.g., the first nucleotide, the secondnucleotide, the third nucleotide, the fourth nucleotide, the fifthnucleotide, the sixth nucleotide, the seventh nucleotide, the eighthnucleotide, the ninth nucleotide, the tenth nucleotide, the eleventhnucleotide, the twelfth nucleotide, the thirteenth nucleotide, thefourteenth nucleotide, the fifteenth nucleotide, the sixteenthnucleotide, the seventeenth nucleotide, the eighteenth nucleotide, thenineteenth nucleotide, or the twentieth nucleotide of the ribonucleicacid.

In some embodiments, the at least one additional ribonucleic aciddescribed above comprises at least a 12 nucleotide fragment of aribonucleic acid sequence of any of FIGS. 1-15. In some embodiments, theat least one additional ribonucleic acid described above comprises atleast a 12 nucleotide fragment of a sequence with a single nucleotidemismatch to a sequence selected from the group consisting of aribonucleic acid sequence of any of FIGS. 1-15. In some embodiments, theat least one additional ribonucleic acid described above comprises atleast a 12 nucleotide fragment of a ribonucleic acid sequence of any ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In some embodiments, the atleast one additional ribonucleic acid described above comprises at leasta 12 nucleotide fragment of a sequence with a single nucleotide mismatchto a ribonucleic acid sequence of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO:5321). For example, if the target sequence is GATGCTCAGTACAGCCACCTTGG(SEQ ID NO: 5323), the ribonucleic acid sequence of the at least oneadditional ribonucleic acid which comprises at least a 12 nucleotidefragment is GTACAGCCACCT (SEQ ID NO: 5327).

In some embodiments, the ribonucleic acid sequence of the at least oneadditional ribonucleic acid described above comprises at least a 13nucleotide fragment of a ribonucleic acid sequence of any of FIGS. 1-15.In some embodiments, the ribonucleic acid sequence of the at least oneadditional ribonucleic acid described above comprises at least a 13nucleotide fragment of a sequence with a single nucleotide mismatch to asequence selected from the group consisting of a ribonucleic acidsequence of any of FIGS. 1-15. In some embodiments, the ribonucleic acidsequence of the at least one additional ribonucleic acid described abovecomprises at least a 13 nucleotide fragment of a ribonucleic acidsequence of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In someembodiments, the ribonucleic acid sequence of the at least oneadditional ribonucleic acid described above comprises at least a 13nucleotide fragment of a sequence with a single nucleotide mismatch to aribonucleic acid sequence of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321).For example, if the target sequence is GATGCTCAGTACAGCCACCTTGG (SEQ IDNO: 5323), the ribonucleic acid sequence of the at least one additionalribonucleic acid which comprises at least a 13 nucleotide fragment isAGTACAGCCACCT (SEQ ID NO: 5328).

In some embodiments, the ribonucleic acid sequence of the at least oneadditional ribonucleic acid described above comprises at least a 14nucleotide fragment of a ribonucleic acid sequence of any of FIGS. 1-15.In some embodiments, the ribonucleic acid sequence of the at least oneadditional ribonucleic acid described above comprises at least a 14nucleotide fragment of a sequence with a single nucleotide mismatch to asequence selected from the group consisting of a ribonucleic acidsequence of any of FIGS. 1-15. In some embodiments, the ribonucleic acidsequence of the at least one additional ribonucleic acid described abovecomprises at least a 14 nucleotide fragment of a ribonucleic acidsequence of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In someembodiments, the ribonucleic acid sequence of the at least oneadditional ribonucleic acid described above comprises at least a 14nucleotide fragment of a sequence with a single nucleotide mismatch to aribonucleic acid sequence of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321).For example, if the target sequence is GATGCTCAGTACAGCCACCTTGG (SEQ IDNO: 5323), the ribonucleic acid sequence of the at least one additionalribonucleic acid which comprises at least a 14 nucleotide fragment isCAGTACAGCCACCT (SEQ ID NO: 5329).

In some embodiments, the ribonucleic acid sequence of the at least oneadditional ribonucleic acid described above comprises at least a 15nucleotide fragment of a ribonucleic acid sequence of any of FIGS. 1-15.In some embodiments, the ribonucleic acid sequence of the at least oneadditional ribonucleic acid described above comprises at least a 15nucleotide fragment of a sequence with a single nucleotide mismatch to asequence selected from the group consisting of a ribonucleic acidsequence of any of FIGS. 1-15. In some embodiments, the ribonucleic acidsequence of the at least one additional ribonucleic acid described abovecomprises at least a 15 nucleotide fragment of a ribonucleic acidsequence of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In someembodiments, the ribonucleic acid sequence of the at least oneadditional ribonucleic acid described above comprises at least a 15nucleotide fragment of a sequence with a single nucleotide mismatch to aribonucleic acid sequence of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321).For example, if the target sequence is GATGCTCAGTACAGCCACCTTGG (SEQ IDNO: 5323), the ribonucleic acid sequence of the at least one additionalribonucleic acid which comprises at least a 15 nucleotide fragment isTCAGTACAGCCACCT (SEQ ID NO: 5330).

In some embodiments, the ribonucleic acid sequence of the at least oneadditional ribonucleic acid described above comprise at least a 16nucleotide fragment of a ribonucleic acid sequence of any of FIGS. 1-15.In some embodiments, the ribonucleic acid sequence of the at least oneadditional ribonucleic acid described above comprises at least a 16nucleotide fragment of a sequence with a single nucleotide mismatch to asequence selected from the group consisting of a ribonucleic acidsequence of any of FIGS. 1-15. In some embodiments, the ribonucleic acidsequence of the at least one additional ribonucleic acid described abovecomprise at least a 16 nucleotide fragment of a ribonucleic acidsequence of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In someembodiments, the ribonucleic acid sequence of the at least oneadditional ribonucleic acid described above comprises at least a 16nucleotide fragment of a sequence with a single nucleotide mismatch to aribonucleic acid sequence of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321).For example, if the target sequence is GATGCTCAGTACAGCCACCTTGG (SEQ IDNO: 5323), the ribonucleic acid sequence of the at least one additionalribonucleic acid which comprises at least a 16 nucleotide fragment isCTCAGTACAGCCACCT (SEQ ID NO: 5331).

In some embodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 17 nucleotidefragment of a ribonucleic acid sequence of any of FIGS. 1-15. In someembodiments, the ribonucleic acid sequence of the at least oneadditional ribonucleic acid described above comprises at least a 17nucleotide fragment of a sequence with a single nucleotide mismatch to asequence selected from the group consisting of a ribonucleic acidsequence of any of FIGS. 1-15. In some embodiments, the ribonucleic acidsequence of the at least one ribonucleic acid described above comprisesat least a 17 nucleotide fragment of a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In some embodiments, theribonucleic acid sequence of the at least one additional ribonucleicacid described above comprises at least a 17 nucleotide fragment of asequence with a single nucleotide mismatch to a ribonucleic acidsequence of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). For example, ifthe target sequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), theribonucleic acid sequence of the at least one additional ribonucleicacid which comprises at least a 17 nucleotide fragment isGCTCAGTACAGCCACCT (SEQ ID NO: 5332).

In some embodiments, the ribonucleic acid sequence of the at least oneadditional ribonucleic acid described above comprises at least a 18nucleotide fragment of a ribonucleic acid sequence of any of FIGS. 1-15.In some embodiments, the ribonucleic acid sequence of the at least oneadditional ribonucleic acid described above comprises at least a 18nucleotide fragment of a sequence with a single nucleotide mismatch to asequence selected from the group consisting of a ribonucleic acidsequence of any of FIGS. 1-15. In some embodiments, the ribonucleic acidsequence of the at least one additional ribonucleic acid described abovecomprises at least a 18 nucleotide fragment of a ribonucleic acidsequence of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In someembodiments, the ribonucleic acid sequence of the at least oneadditional ribonucleic acid described above comprises at least a 18nucleotide fragment of a sequence with a single nucleotide mismatch to aribonucleic acid sequence of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321).For example, if the target sequence is GATGCTCAGTACAGCCACCTTGG (SEQ IDNO: 5323), the ribonucleic acid sequence of the at least one additionalribonucleic acid which comprises at least a 18 nucleotide fragment isTGCTCAGTACAGCCACCT (SEQ ID NO: 5333).

In some embodiments, the ribonucleic acid sequence of the at least oneadditional ribonucleic acid described above comprise at least a 19nucleotide fragment of a ribonucleic acid sequence of any of FIGS. 1-15.In some embodiments, the ribonucleic acid sequence of the at least oneadditional ribonucleic acid described above comprises at least a 19nucleotide fragment of a sequence with a single nucleotide mismatch to asequence selected from the group consisting of a ribonucleic acidsequence of any of FIGS. 1-15. In some embodiments, the ribonucleic acidsequence of the at least one additional ribonucleic acid described abovecomprise at least a 19 nucleotide fragment of a ribonucleic acidsequence of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In someembodiments, the ribonucleic acid sequence of the at least oneadditional ribonucleic acid described above comprises at least a 19nucleotide fragment of a sequence with a single nucleotide mismatch to aribonucleic acid sequence of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321).For example, if the target sequence is GATGCTCAGTACAGCCACCTTGG (SEQ IDNO: 5323), the ribonucleic acid sequence of the at least one additionalribonucleic acid which comprises at least a 19 nucleotide fragment isATGCTCAGTACAGCCACCT (SEQ ID NO: 5334).

In some embodiments, the ribonucleic acid sequence of the at least oneadditional ribonucleic acid described above comprises at least a 20nucleotide fragment of a ribonucleic acid sequence of any of FIGS. 1-15.In some embodiments, the ribonucleic acid sequence of the at least oneadditional ribonucleic acid described above comprises at least a 20nucleotide fragment of a sequence with a single nucleotide mismatch to asequence selected from the group consisting of a ribonucleic acidsequence of any of FIGS. 1-15. In some embodiments, the ribonucleic acidsequence of the at least one additional ribonucleic acid described abovecomprises at least a 20 nucleotide fragment of a ribonucleic acidsequence of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In someembodiments, the ribonucleic acid sequence of the at least oneadditional ribonucleic acid described above comprises at least a 20nucleotide fragment of a sequence with a single nucleotide mismatch to aribonucleic acid sequence of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321).For example, if the target sequence is GATGCTCAGTACAGCCACCTTGG (SEQ IDNO: 5323), the ribonucleic acid sequence of the at least one additionalribonucleic acid which comprises at least a 20 nucleotide fragment isGATGCTCAGTACAGCCACCT (SEQ ID NO: 5324).

In some aspects, the present invention provides a composition comprisinga chimeric nucleic acid comprising a ribonucleic acid encoding a Casprotein and at least one additional ribonucleic acid sequence comprisinga sequence with a single nucleotide mismatch to a sequence selected fromthe group consisting of the ribonucleic acid sequences of FIG. 1.

In some aspects, the present invention provides a composition comprisinga chimeric nucleic acid comprising a ribonucleic acid encoding a Casprotein and at least one additional ribonucleic acid sequence comprisinga sequence with a single nucleotide mismatch to a sequence selected fromthe group consisting of the ribonucleic acid sequences of FIG. 2.

In some aspects, the present invention provides a composition comprisinga chimeric nucleic acid comprising a ribonucleic acid encoding a Casprotein and at least one additional ribonucleic acid sequence comprisinga sequence with a single nucleotide mismatch to a sequence selected fromthe group consisting of the ribonucleic acid sequences of FIG. 3.

In some aspects, the present invention provides a composition comprisinga chimeric nucleic acid comprising a ribonucleic acid encoding a Casprotein and at least one additional ribonucleic acid sequence comprisinga sequence with a single nucleotide mismatch to a sequence selected fromthe group consisting of the ribonucleic acid sequences of FIG. 4.

In some aspects, the present invention provides a composition comprisinga chimeric nucleic acid comprising a ribonucleic acid encoding a Casprotein and at least one additional ribonucleic acid sequence comprisinga sequence with a single nucleotide mismatch to a sequence selected fromthe group consisting of the ribonucleic acid sequences of FIG. 5.

In some aspects, the present invention provides a composition comprisinga chimeric nucleic acid comprising a ribonucleic acid encoding a Casprotein and at least one additional ribonucleic acid sequence comprisinga sequence with a single nucleotide mismatch to a sequence selected fromthe group consisting of the ribonucleic acid sequences of FIG. 6.

In some aspects, the present invention provides a composition comprisinga chimeric nucleic acid comprising a ribonucleic acid encoding a Casprotein and at least one additional ribonucleic acid sequence comprisinga sequence with a single nucleotide mismatch to a sequence selected fromthe group consisting of the ribonucleic acid sequences of FIG. 7.

In some aspects, the present invention provides a composition comprisinga chimeric nucleic acid comprising a ribonucleic acid encoding a Casprotein and at least one additional ribonucleic acid sequence comprisinga sequence with a single nucleotide mismatch to a sequence selected fromthe group consisting of the ribonucleic acid sequences of FIG. 8.

In some aspects, the present invention provides a composition comprisinga chimeric nucleic acid comprising a ribonucleic acid encoding a Casprotein and at least one additional ribonucleic acid sequence comprisinga sequence with a single nucleotide mismatch to a sequence selected fromthe group consisting of the ribonucleic acid sequences of FIG. 9.

In some aspects, the present invention provides a composition comprisinga chimeric nucleic acid comprising a ribonucleic acid encoding a Casprotein and at least one additional ribonucleic acid sequence comprisinga sequence with a single nucleotide mismatch to a sequence selected fromthe group consisting of the ribonucleic acid sequences of FIG. 10.

In some aspects, the present invention provides a composition comprisinga chimeric nucleic acid comprising a ribonucleic acid encoding a Casprotein and at least one additional ribonucleic acid sequence comprisinga sequence with a single nucleotide mismatch to a sequence selected fromthe group consisting of the ribonucleic acid sequences of FIG. 11.

In some aspects, the present invention provides a composition comprisinga chimeric nucleic acid comprising a ribonucleic acid encoding a Casprotein and at least one additional ribonucleic acid sequence comprisinga sequence with a single nucleotide mismatch to a sequence selected fromthe group consisting of the ribonucleic acid sequences of FIG. 12.

In some aspects, the present invention provides a composition comprisinga chimeric nucleic acid comprising a ribonucleic acid encoding a Casprotein and at least one additional ribonucleic acid sequence comprisinga sequence with a single nucleotide mismatch to a sequence selected fromthe group consisting of the ribonucleic acid sequences of FIG. 13.

In some aspects, the present invention provides a composition comprisinga chimeric nucleic acid comprising a ribonucleic acid encoding a Casprotein and at least one additional ribonucleic acid sequence comprisinga sequence with a single nucleotide mismatch to a sequence selected fromthe group consisting of the ribonucleic acid sequences of FIG. 14.

In some aspects, the present invention provides a composition comprisinga chimeric nucleic acid comprising a ribonucleic acid encoding a Casprotein and at least one additional ribonucleic acid sequence comprisinga sequence with a single nucleotide mismatch to a sequence selected fromthe group consisting of the ribonucleic acid sequences of FIG. 15.

In some aspects, the present invention provides a composition comprisinga chimeric nucleic acid comprising a ribonucleic acid encoding a Casprotein and at least one additional ribonucleic acid sequence comprisinga sequence with a single nucleotide mismatch to a ribonucleic acidsequence of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321).

In some embodiments, the at least one additional ribonucleic acidsequences described above do not include the 3 nucleotide NGG sequence.For example, if the target site sequence is GATGCTCAGTACAGCCACCTTGG (SEQID NO: 5323), the ribonucleic acid sequence of the at least oneadditional ribonucleic acid is GATGCTCAGTACAGCCACCT (SEQ ID NO: 5324).As another example, if the target sequence is GATGCTCAGTACAGCCACCTTGG(SEQ ID NO: 5323), a ribonucleic acid sequence with a single nucleotidemismatch which does not include the 3 nucleotide NGG sequence isGATGCTGAGTACAGCCACCT (SEQ ID NO: 5326), with the italicized G being themismatched nucleotide. Those skilled in the art will appreciate,however, that the single nucleotide mismatch can comprise any nucleotidein the ribonucleic acid, e.g., the first nucleotide, the secondnucleotide, the third nucleotide, the fourth nucleotide, the fifthnucleotide, the sixth nucleotide, the seventh nucleotide, the eighthnucleotide, the ninth nucleotide, the tenth nucleotide, the eleventhnucleotide, the twelfth nucleotide, the thirteenth nucleotide, thefourteenth nucleotide, the fifteenth nucleotide, the sixteenthnucleotide, the seventeenth nucleotide, the eighteenth nucleotide, thenineteenth nucleotide, or the twentieth nucleotide of the ribonucleicacid.

In some embodiments, the at least one additional ribonucleic aciddescribed above comprises at least a 12 nucleotide fragment of aribonucleic acid sequence of any of FIGS. 1-15. In some embodiments, theat least one additional ribonucleic acid described above comprises atleast a 12 nucleotide fragment of a sequence with a single nucleotidemismatch to a sequence selected from the group consisting of aribonucleic acid sequence of any of FIGS. 1-15. In some embodiments, theat least one additional ribonucleic acid described above comprises atleast a 12 nucleotide fragment of a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In some embodiments, the atleast one additional ribonucleic acid described above comprises at leasta 12 nucleotide fragment of a sequence with a single nucleotide mismatchto a sequence selected from the group consisting of a ribonucleic acidsequence of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). For example, ifthe target sequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), theribonucleic acid sequence of the at least one additional ribonucleicacid which comprises at least a 12 nucleotide fragment is GTACAGCCACCT(SEQ ID NO: 5327).

In some embodiments, the ribonucleic acid sequence of the at least oneadditional ribonucleic acid described above comprises at least a 13nucleotide fragment of a ribonucleic acid sequence of any of FIGS. 1-15.In some embodiments, the ribonucleic acid sequence of the at least oneadditional ribonucleic acid described above comprises at least a 13nucleotide fragment of a sequence with a single nucleotide mismatch to asequence selected from the group consisting of a ribonucleic acidsequence of any of FIGS. 1-15. In some embodiments, the ribonucleic acidsequence of the at least one additional ribonucleic acid described abovecomprises at least a 13 nucleotide fragment of a ribonucleic acidsequence of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In someembodiments, the ribonucleic acid sequence of the at least oneadditional ribonucleic acid described above comprises at least a 13nucleotide fragment of a sequence with a single nucleotide mismatch to aribonucleic acid sequence of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321).For example, if the target sequence is GATGCTCAGTACAGCCACCTTGG (SEQ IDNO: 5323), the ribonucleic acid sequence of the at least one additionalribonucleic acid which comprises at least a 13 nucleotide fragment isAGTACAGCCACCT (SEQ ID NO: 5328).

In some embodiments, the ribonucleic acid sequence of the at least oneadditional ribonucleic acid described above comprises at least a 14nucleotide fragment of a ribonucleic acid sequence of any of FIGS. 1-15.In some embodiments, the ribonucleic acid sequence of the at least oneadditional ribonucleic acid described above comprises at least a 14nucleotide fragment of a sequence with a single nucleotide mismatch to asequence selected from the group consisting of a ribonucleic acidsequence of any of FIGS. 1-15. In some embodiments, the ribonucleic acidsequence of the at least one additional ribonucleic acid described abovecomprises at least a 14 nucleotide fragment of a ribonucleic acidsequence of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In someembodiments, the ribonucleic acid sequence of the at least oneadditional ribonucleic acid described above comprises at least a 14nucleotide fragment of a sequence with a single nucleotide mismatch to aribonucleic acid sequence of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321).For example, if the target sequence is GATGCTCAGTACAGCCACCTTGG (SEQ IDNO: 5323), the ribonucleic acid sequence of the at least one additionalribonucleic acid which comprises at least a 14 nucleotide fragment isCAGTACAGCCACCT (SEQ ID NO: 5329).

In some embodiments, the ribonucleic acid sequence of the at least oneadditional ribonucleic acid described above comprises at least a 15nucleotide fragment of a ribonucleic acid sequence of any of FIGS. 1-15.In some embodiments, the ribonucleic acid sequence of the at least oneadditional ribonucleic acid described above comprises at least a 15nucleotide fragment of a sequence with a single nucleotide mismatch to asequence selected from the group consisting of a ribonucleic acidsequence of any of FIGS. 1-15. In some embodiments, the ribonucleic acidsequence of the at least one additional ribonucleic acid described abovecomprises at least a 15 nucleotide fragment of a ribonucleic acidsequence of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In someembodiments, the ribonucleic acid sequence of the at least oneadditional ribonucleic acid described above comprises at least a 15nucleotide fragment of a sequence with a single nucleotide mismatch to aribonucleic acid sequence of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321).For example, if the target sequence is GATGCTCAGTACAGCCACCTTGG (SEQ IDNO: 5323), the ribonucleic acid sequence of the at least one additionalribonucleic acid which comprises at least a 15 nucleotide fragment isTCAGTACAGCCACCT (SEQ ID NO: 5330).

In some embodiments, the ribonucleic acid sequence of the at least oneadditional ribonucleic acid described above comprise at least a 16nucleotide fragment of a ribonucleic acid sequence of any of FIGS. 1-15.In some embodiments, the ribonucleic acid sequence of the at least oneadditional ribonucleic acid described above comprises at least a 16nucleotide fragment of a sequence with a single nucleotide mismatch to asequence selected from the group consisting of a ribonucleic acidsequence of any of FIGS. 1-15. In some embodiments, the ribonucleic acidsequence of the at least one additional ribonucleic acid described abovecomprise at least a 16 nucleotide fragment of a ribonucleic acidsequence of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In someembodiments, the ribonucleic acid sequence of the at least oneadditional ribonucleic acid described above comprises at least a 16nucleotide fragment of a sequence with a single nucleotide mismatch to aribonucleic acid sequence of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321).For example, if the target sequence is GATGCTCAGTACAGCCACCTTGG (SEQ IDNO: 5323), the ribonucleic acid sequence of the at least one additionalribonucleic acid which comprises at least a 16 nucleotide fragment isCTCAGTACAGCCACCT (SEQ ID NO: 5331).

In some embodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 17 nucleotidefragment of a ribonucleic acid sequence of any of FIGS. 1-15. In someembodiments, the ribonucleic acid sequence of the at least oneadditional ribonucleic acid described above comprises at least a 17nucleotide fragment of a sequence with a single nucleotide mismatch to asequence selected from the group consisting of a ribonucleic acidsequence of any of FIGS. 1-15. In some embodiments, the ribonucleic acidsequence of the at least one ribonucleic acid described above comprisesat least a 17 nucleotide fragment of a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In some embodiments, theribonucleic acid sequence of the at least one additional ribonucleicacid described above comprises at least a 17 nucleotide fragment of asequence with a single nucleotide mismatch to a ribonucleic acidsequence of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). For example, ifthe target sequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), theribonucleic acid sequence of the at least one additional ribonucleicacid which comprises at least a 17 nucleotide fragment isGCTCAGTACAGCCACCT (SEQ ID NO: 5332).

In some embodiments, the ribonucleic acid sequence of the at least oneadditional ribonucleic acid described above comprises at least a 18nucleotide fragment of a ribonucleic acid sequence of any of FIGS. 1-15.In some embodiments, the ribonucleic acid sequence of the at least oneadditional ribonucleic acid described above comprises at least a 18nucleotide fragment of a sequence with a single nucleotide mismatch to asequence selected from the group consisting of a ribonucleic acidsequence of any of FIGS. 1-15. In some embodiments, the ribonucleic acidsequence of the at least one additional ribonucleic acid described abovecomprises at least a 18 nucleotide fragment of a ribonucleic acidsequence of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In someembodiments, the ribonucleic acid sequence of the at least oneadditional ribonucleic acid described above comprises at least a 18nucleotide fragment of a sequence with a single nucleotide mismatch to aribonucleic acid sequence of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321).For example, if the target sequence is GATGCTCAGTACAGCCACCTTGG (SEQ IDNO: 5323), the ribonucleic acid sequence of the at least one additionalribonucleic acid which comprises at least a 18 nucleotide fragment isTGCTCAGTACAGCCACCT (SEQ ID NO: 5333).

In some embodiments, the ribonucleic acid sequence of the at least oneadditional ribonucleic acid described above comprise at least a 19nucleotide fragment of a ribonucleic acid sequence of any of FIGS. 1-15.In some embodiments, the ribonucleic acid sequence of the at least oneadditional ribonucleic acid described above comprises at least a 19nucleotide fragment of a sequence with a single nucleotide mismatch to asequence selected from the group consisting of a ribonucleic acidsequence of any of FIGS. 1-15. In some embodiments, the ribonucleic acidsequence of the at least one additional ribonucleic acid described abovecomprise at least a 19 nucleotide fragment of a ribonucleic acidsequence of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In someembodiments, the ribonucleic acid sequence of the at least oneadditional ribonucleic acid described above comprises at least a 19nucleotide fragment of a sequence with a single nucleotide mismatch to aribonucleic acid sequence of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321).For example, if the target sequence is GATGCTCAGTACAGCCACCTTGG (SEQ IDNO: 5323), the ribonucleic acid sequence of the at least one additionalribonucleic acid which comprises at least a 19 nucleotide fragment isATGCTCAGTACAGCCACCT (SEQ ID NO: 5334).

In some embodiments, the ribonucleic acid sequence of the at least oneadditional ribonucleic acid described above comprises at least a 20nucleotide fragment of a ribonucleic acid sequence of any of FIGS. 1-15.In some embodiments, the ribonucleic acid sequence of the at least oneadditional ribonucleic acid described above comprises at least a 20nucleotide fragment of a sequence with a single nucleotide mismatch to asequence selected from the group consisting of a ribonucleic acidsequence of any of FIGS. 1-15. In some embodiments, the ribonucleic acidsequence of the at least one additional ribonucleic acid described abovecomprises at least a 20 nucleotide fragment of a ribonucleic acidsequence of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In someembodiments, the ribonucleic acid sequence of the at least oneadditional ribonucleic acid described above comprises at least a 20nucleotide fragment of a sequence with a single nucleotide mismatch to aribonucleic acid sequence of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321).For example, if the target sequence is GATGCTCAGTACAGCCACCTTGG (SEQ IDNO: 5323), the ribonucleic acid sequence of the at least one additionalribonucleic acid which comprises at least a 20 nucleotide fragment isGATGCTCAGTACAGCCACCT (SEQ ID NO: 5324).

In some embodiments, a composition of the present invention comprises anucleic acid sequence encoding a fluorescent protein selected from thegroup consisting of green fluorescent protein and red fluorescentprotein. In some embodiments, a composition of the present inventioncomprises a promoter operably linked to the chimeric nucleic acid. Insome embodiments, the promoter is optimized for increased expression inhuman stem cells. In some embodiments, the promoter is selected from thegroup consisting of a Cytomegalovirus (CMV) early enhancer element and achicken beta-actin promoter, a chicken beta-actin promoter, anelongation factor-1 alpha promoter, and a ubiquitin promoter.

In some embodiments, the chimeric nucleic acid is contained in ananoparticle. In some embodiments, the chimeric nucleic acid iscontained in a lipid nanoparticle as described herein. In someembodiments, the chimeric nucleic acid comprises at least one modifiednucleotide described herein. In some embodiments, the Cas proteincomprises a Cas9 protein or a functional portion thereof.

For in vivo methods, a therapeutically effective amount of a compositiondescribed herein can be administered to a subject. Methods ofadministering compositions to a subject are known in the art and easilyavailable to one of skill in the art.

In some embodiments, a composition described herein includes one or moreadditional pharmaceutically active agents for treating or preventing thedisorder associated with expression of the target polynucleotidesequence.

The present invention also provides kits for practicing any of themethods of the present invention, as well as kits comprising thecompositions of the present invention, and instructions for using thekits for altering target polynucleotide sequences in a cell.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence selected from the group consisting of the ribonucleic acidsequences of FIG. 1.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence selected from the group consisting of the ribonucleic acidsequences of FIG. 2.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence selected from the group consisting of the ribonucleic acidsequences of FIG. 3.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence selected from the group consisting of the ribonucleic acidsequences of FIG. 4.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence selected from the group consisting of the ribonucleic acidsequences of FIG. 5.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence selected from the group consisting of the ribonucleic acidsequences of FIG. 6.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence selected from the group consisting of the ribonucleic acidsequences of FIG. 7.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence selected from the group consisting of the ribonucleic acidsequences of FIG. 8.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence selected from the group consisting of the ribonucleic acidsequences of FIG. 9.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence selected from the group consisting of the ribonucleic acidsequences of FIG. 10.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence selected from the group consisting of the ribonucleic acidsequences of FIG. 11.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence selected from the group consisting of the ribonucleic acidsequences of FIG. 12.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence selected from the group consisting of the ribonucleic acidsequences of FIG. 13.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence selected from the group consisting of the ribonucleic acidsequences of FIG. 14.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence selected from the group consisting of the ribonucleic acidsequences of FIG. 15.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence having a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321).

In some embodiments, the at least one ribonucleic acid sequencesdescribed above do not include the 3 nucleotide NGG sequence. Forexample, if the target site sequence is GATGCTCAGTACAGCCACCTTGG (SEQ IDNO: 5323), the ribonucleic acid sequence of the at least one ribonucleicacid sequence is GATGCTCAGTACAGCCACCT (SEQ ID NO: 5324). As anotherexample, if the target sequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO:5323), a ribonucleic acid sequence with a single nucleotide mismatchwhich does not include the 3 nucleotide NGG sequence isGATGCTGAGTACAGCCACCT (SEQ ID NO: 5326), with the italicized G being themismatched nucleotide. Those skilled in the art will appreciate,however, that the single nucleotide mismatch can comprise any nucleotidein the ribonucleic acid, e.g., the first nucleotide, the secondnucleotide, the third nucleotide, the fourth nucleotide, the fifthnucleotide, the sixth nucleotide, the seventh nucleotide, the eighthnucleotide, the ninth nucleotide, the tenth nucleotide, the eleventhnucleotide, the twelfth nucleotide, the thirteenth nucleotide, thefourteenth nucleotide, the fifteenth nucleotide, the sixteenthnucleotide, the seventeenth nucleotide, the eighteenth nucleotide, thenineteenth nucleotide, or the twentieth nucleotide of the ribonucleicacid.

In some embodiments, the at least one ribonucleic acid described abovecomprises at least a 12 nucleotide fragment of a ribonucleic acidsequence of any of FIGS. 1-15. In some embodiments, the at least oneribonucleic acid described above comprises at least a 12 nucleotidefragment of a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of a ribonucleic acid sequence of anyof FIGS. 1-15. In some embodiments, the at least one ribonucleic aciddescribed above comprises at least a 12 nucleotide fragment of aribonucleic acid sequence of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321).In some embodiments, the at least one ribonucleic acid described abovecomprises at least a 12 nucleotide fragment of a sequence with a singlenucleotide mismatch to a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). For example, if the targetsequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleicacid sequence of the at least one ribonucleic acid which comprises atleast a 12 nucleotide fragment is GTACAGCCACCT (SEQ ID NO: 5327).

In some embodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 13 nucleotidefragment of a ribonucleic acid sequence of any of FIGS. 1-15. In someembodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 13 nucleotidefragment of a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of a ribonucleic acid sequence of anyof FIGS. 1-15. In some embodiments, the ribonucleic acid sequence of theat least one ribonucleic acid described above comprises at least a 13nucleotide fragment of a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In some embodiments, theribonucleic acid sequence of the at least one ribonucleic acid describedabove comprises at least a 13 nucleotide fragment of a sequence with asingle nucleotide mismatch to f a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). For example, if the targetsequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleicacid sequence of the at least one ribonucleic acid which comprises atleast a 13 nucleotide fragment is AGTACAGCCACCT (SEQ ID NO: 5328).

In some embodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 14 nucleotidefragment of a ribonucleic acid sequence of any of FIGS. 1-15. In someembodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 14 nucleotidefragment of a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of a ribonucleic acid sequence of anyof FIGS. 1-15. In some embodiments, the ribonucleic acid sequence of theat least one ribonucleic acid described above comprises at least a 14nucleotide fragment of a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In some embodiments, theribonucleic acid sequence of the at least one ribonucleic acid describedabove comprises at least a 14 nucleotide fragment of a sequence with asingle nucleotide mismatch to a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). For example, if the targetsequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleicacid sequence of the at least one ribonucleic acid which comprises atleast a 14 nucleotide fragment is CAGTACAGCCACCT (SEQ ID NO: 5329).

In some embodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 15 nucleotidefragment of a ribonucleic acid sequence of any of FIGS. 1-15. In someembodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 15 nucleotidefragment of a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of a ribonucleic acid sequence of anyof FIGS. 1-15. In some embodiments, the ribonucleic acid sequence of theat least one ribonucleic acid described above comprises at least a 15nucleotide fragment of a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In some embodiments, theribonucleic acid sequence of the at least one ribonucleic acid describedabove comprises at least a 15 nucleotide fragment of a sequence with asingle nucleotide mismatch to a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). For example, if the targetsequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleicacid sequence of the at least one ribonucleic acid which comprises atleast a 15 nucleotide fragment is TCAGTACAGCCACCT (SEQ ID NO: 5330).

In some embodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprise at least a 16 nucleotidefragment of a ribonucleic acid sequence of any of FIGS. 1-15. In someembodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 16 nucleotidefragment of a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of a ribonucleic acid sequence of anyof FIGS. 1-15. In some embodiments, the ribonucleic acid sequence of theat least one ribonucleic acid described above comprise at least a 16nucleotide fragment of a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In some embodiments, theribonucleic acid sequence of the at least one ribonucleic acid describedabove comprises at least a 16 nucleotide fragment of a sequence with asingle nucleotide mismatch to a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). For example, if the targetsequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleicacid sequence of the at least one ribonucleic acid which comprises atleast a 16 nucleotide fragment is CTCAGTACAGCCACCT (SEQ ID NO: 5331).

In some embodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 17 nucleotidefragment of a ribonucleic acid sequence of any of FIGS. 1-15. In someembodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 17 nucleotidefragment of a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of a ribonucleic acid sequence of anyof FIGS. 1-15. In some embodiments, the ribonucleic acid sequence of theat least one ribonucleic acid described above comprises at least a 17nucleotide fragment of a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In some embodiments, theribonucleic acid sequence of the at least one ribonucleic acid describedabove comprises at least a 17 nucleotide fragment of a sequence with asingle nucleotide mismatch to a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). For example, if the targetsequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleicacid sequence of the at least one ribonucleic acid which comprises atleast a 17 nucleotide fragment is GCTCAGTACAGCCACCT (SEQ ID NO: 5332).

In some embodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 18 nucleotidefragment of a ribonucleic acid sequence of any of FIGS. 1-15. In someembodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 18 nucleotidefragment of a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of a ribonucleic acid sequence of anyof FIGS. 1-15. In some embodiments, the ribonucleic acid sequence of theat least one ribonucleic acid described above comprises at least a 18nucleotide fragment of a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In some embodiments, theribonucleic acid sequence of the at least one ribonucleic acid describedabove comprises at least a 18 nucleotide fragment of a sequence with asingle nucleotide mismatch to a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). For example, if the targetsequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleicacid sequence of the at least one ribonucleic acid which comprises atleast a 18 nucleotide fragment is TGCTCAGTACAGCCACCT (SEQ ID NO: 5333).

In some embodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprise at least a 19 nucleotidefragment of a ribonucleic acid sequence of any of FIGS. 1-15. In someembodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 19 nucleotidefragment of a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of a ribonucleic acid sequence of anyof FIGS. 1-15. In some embodiments, the ribonucleic acid sequence of theat least one ribonucleic acid described above comprise at least a 19nucleotide fragment of a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In some embodiments, theribonucleic acid sequence of the at least one ribonucleic acid describedabove comprises at least a 19 nucleotide fragment of a sequence with asingle nucleotide mismatch to a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). For example, if the targetsequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleicacid sequence of the at least one ribonucleic acid which comprises atleast a 19 nucleotide fragment is ATGCTCAGTACAGCCACCT (SEQ ID NO: 5334).

In some embodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 20 nucleotidefragment of a ribonucleic acid sequence of any of FIGS. 1-15. In someembodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 20 nucleotidefragment of a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of a ribonucleic acid sequence of anyof FIGS. 1-15. In some embodiments, the ribonucleic acid sequence of theat least one ribonucleic acid described above comprises at least a 20nucleotide fragment of a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In some embodiments, theribonucleic acid sequence of the at least one ribonucleic acid describedabove comprises at least a 20 nucleotide fragment of a sequence with asingle nucleotide mismatch to a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). For example, if the targetsequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleicacid sequence of the at least one ribonucleic acid which comprises atleast a 20 nucleotide fragment is GATGCTCAGTACAGCCACCT (SEQ ID NO:5324).

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence with a single nucleotide mismatch to a ribonucleic acidsequence selected from the group consisting of the ribonucleic acidsequences of FIG. 1, and any combination thereof.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence with a single nucleotide mismatch to a ribonucleic acidsequence selected from the group consisting of the ribonucleic acidsequences of FIG. 2, and any combination thereof.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence with a single nucleotide mismatch to a ribonucleic acidsequence selected from the group consisting of the ribonucleic acidsequences of FIG. 3, and any combination thereof.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence with a single nucleotide mismatch to a ribonucleic acidsequence selected from the group consisting of the ribonucleic acidsequences of FIG. 4, and any combination thereof.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence with a single nucleotide mismatch to a ribonucleic acidsequence selected from the group consisting of the ribonucleic acidsequences of FIG. 5, and any combination thereof.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence with a single nucleotide mismatch to a ribonucleic acidsequence selected from the group consisting of the ribonucleic acidsequences of FIG. 6, and any combination thereof.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence with a single nucleotide mismatch to a ribonucleic acidsequence selected from the group consisting of the ribonucleic acidsequences of FIG. 7, and any combination thereof.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence with a single nucleotide mismatch to a ribonucleic acidsequence selected from the group consisting of the ribonucleic acidsequences of FIG. 8, and any combination thereof.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence with a single nucleotide mismatch to a ribonucleic acidsequence selected from the group consisting of the ribonucleic acidsequences of FIG. 9, and any combination thereof.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence with a single nucleotide mismatch to a ribonucleic acidsequence selected from the group consisting of the ribonucleic acidsequences of FIG. 10, and any combination thereof.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence with a single nucleotide mismatch to a ribonucleic acidsequence selected from the group consisting of the ribonucleic acidsequences of FIG. 11, and any combination thereof.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence with a single nucleotide mismatch to a ribonucleic acidsequence selected from the group consisting of the ribonucleic acidsequences of FIG. 12, and any combination thereof.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence with a single nucleotide mismatch to a ribonucleic acidsequence selected from the group consisting of the ribonucleic acidsequences of FIG. 13, and any combination thereof.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence with a single nucleotide mismatch to a ribonucleic acidsequence selected from the group consisting of the ribonucleic acidsequences of FIG. 14, and any combination thereof.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence with a single nucleotide mismatch to a ribonucleic acidsequence selected from the group consisting of the ribonucleic acidsequences of FIG. 15, and any combination thereof.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence with a single nucleotide mismatch to a ribonucleic acidsequence of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321).

In some embodiments, the at least one ribonucleic acid sequences withthe single nucleotide mismatches described above do not include the 3nucleotide NGG sequence. For example, if the target site sequence isGATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleic acid sequenceof the at least one ribonucleic acid sequence is GATGCTCAGTACAGCCACCT(SEQ ID NO: 5324). As another example, if the target sequence isGATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), a ribonucleic acid sequencewith a single nucleotide mismatch which does not include the 3nucleotide NGG sequence is GATGCTGAGTACAGCCACCT (SEQ ID NO: 5326), withthe italicized G being the mismatched nucleotide. Those skilled in theart will appreciate, however, that the single nucleotide mismatch cancomprise any nucleotide in the ribonucleic acid, e.g., the firstnucleotide, the second nucleotide, the third nucleotide, the fourthnucleotide, the fifth nucleotide, the sixth nucleotide, the seventhnucleotide, the eighth nucleotide, the ninth nucleotide, the tenthnucleotide, the eleventh nucleotide, the twelfth nucleotide, thethirteenth nucleotide, the fourteenth nucleotide, the fifteenthnucleotide, the sixteenth nucleotide, the seventeenth nucleotide, theeighteenth nucleotide, the nineteenth nucleotide, or the twentiethnucleotide of the ribonucleic acid.

In some embodiments, the at least one ribonucleic acid described abovecomprises at least a 12 nucleotide fragment of a ribonucleic acidsequence of any of FIGS. 1-15. In some embodiments, the at least oneribonucleic acid described above comprises at least a 12 nucleotidefragment of a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of a ribonucleic acid sequence of anyof FIGS. 1-15. In some embodiments, the at least one ribonucleic aciddescribed above comprises at least a 12 nucleotide fragment of aribonucleic acid sequence of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321).In some embodiments, the at least one ribonucleic acid described abovecomprises at least a 12 nucleotide fragment of a sequence with a singlenucleotide mismatch to a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). For example, if the targetsequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleicacid sequence of the at least one ribonucleic acid which comprises atleast a 12 nucleotide fragment is GTACAGCCACCT (SEQ ID NO: 5327).

In some embodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 13 nucleotidefragment of a ribonucleic acid sequence of any of FIGS. 1-15. In someembodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 13 nucleotidefragment of a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of a ribonucleic acid sequence of anyof FIGS. 1-15. In some embodiments, the ribonucleic acid sequence of theat least one ribonucleic acid described above comprises at least a 13nucleotide fragment of a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In some embodiments, theribonucleic acid sequence of the at least one ribonucleic acid describedabove comprises at least a 13 nucleotide fragment of a sequence with asingle nucleotide mismatch to a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). For example, if the targetsequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleicacid sequence of the at least one ribonucleic acid which comprises atleast a 13 nucleotide fragment is AGTACAGCCACCT (SEQ ID NO: 5328).

In some embodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 14 nucleotidefragment of a ribonucleic acid sequence of any of FIGS. 1-15. In someembodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 14 nucleotidefragment of a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of a ribonucleic acid sequence of anyof FIGS. 1-15. In some embodiments, the ribonucleic acid sequence of theat least one ribonucleic acid described above comprises at least a 14nucleotide fragment of a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In some embodiments, theribonucleic acid sequence of the at least one ribonucleic acid describedabove comprises at least a 14 nucleotide fragment of a sequence with asingle nucleotide mismatch to a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). For example, if the targetsequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleicacid sequence of the at least one ribonucleic acid which comprises atleast a 14 nucleotide fragment is CAGTACAGCCACCT (SEQ ID NO: 5329).

In some embodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 15 nucleotidefragment of a ribonucleic acid sequence of any of FIGS. 1-15. In someembodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 15 nucleotidefragment of a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of a ribonucleic acid sequence of anyof FIGS. 1-15. In some embodiments, the ribonucleic acid sequence of theat least one ribonucleic acid described above comprises at least a 15nucleotide fragment of a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In some embodiments, theribonucleic acid sequence of the at least one ribonucleic acid describedabove comprises at least a 15 nucleotide fragment of a sequence with asingle nucleotide mismatch to a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). For example, if the targetsequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleicacid sequence of the at least one ribonucleic acid which comprises atleast a 15 nucleotide fragment is TCAGTACAGCCACCT (SEQ ID NO: 5330).

In some embodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprise at least a 16 nucleotidefragment of a ribonucleic acid sequence of any of FIGS. 1-15. In someembodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 16 nucleotidefragment of a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of a ribonucleic acid sequence of anyof FIGS. 1-15. In some embodiments, the ribonucleic acid sequence of theat least one ribonucleic acid described above comprise at least a 16nucleotide fragment of a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In some embodiments, theribonucleic acid sequence of the at least one ribonucleic acid describedabove comprises at least a 16 nucleotide fragment of a sequence with asingle nucleotide mismatch to a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). For example, if the targetsequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleicacid sequence of the at least one ribonucleic acid which comprises atleast a 16 nucleotide fragment is CTCAGTACAGCCACCT (SEQ ID NO: 5331).

In some embodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 17 nucleotidefragment of a ribonucleic acid sequence of any of FIGS. 1-15. In someembodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 17 nucleotidefragment of a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of a ribonucleic acid sequence of anyof FIGS. 1-15. In some embodiments, the ribonucleic acid sequence of theat least one ribonucleic acid described above comprises at least a 17nucleotide fragment of a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In some embodiments, theribonucleic acid sequence of the at least one ribonucleic acid describedabove comprises at least a 17 nucleotide fragment of a sequence with asingle nucleotide mismatch to a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). For example, if the targetsequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleicacid sequence of the at least one ribonucleic acid which comprises atleast a 17 nucleotide fragment is GCTCAGTACAGCCACCT (SEQ ID NO: 5332).

In some embodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 18 nucleotidefragment of a ribonucleic acid sequence of any of FIGS. 1-15. In someembodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 18 nucleotidefragment of a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of a ribonucleic acid sequence of anyof FIGS. 1-15. In some embodiments, the ribonucleic acid sequence of theat least one ribonucleic acid described above comprises at least a 18nucleotide fragment of a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In some embodiments, theribonucleic acid sequence of the at least one ribonucleic acid describedabove comprises at least a 18 nucleotide fragment of a sequence with asingle nucleotide mismatch to a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). For example, if the targetsequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleicacid sequence of the at least one ribonucleic acid which comprises atleast a 18 nucleotide fragment is TGCTCAGTACAGCCACCT (SEQ ID NO: 5333).

In some embodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprise at least a 19 nucleotidefragment of a ribonucleic acid sequence of any of FIGS. 1-15. In someembodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 19 nucleotidefragment of a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of a ribonucleic acid sequence of anyof FIGS. 1-15. In some embodiments, the ribonucleic acid sequence of theat least one ribonucleic acid described above comprise at least a 19nucleotide fragment of a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In some embodiments, theribonucleic acid sequence of the at least one ribonucleic acid describedabove comprises at least a 19 nucleotide fragment of a sequence with asingle nucleotide mismatch to a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). For example, if the targetsequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleicacid sequence of the at least one ribonucleic acid which comprises atleast a 19 nucleotide fragment is ATGCTCAGTACAGCCACCT (SEQ ID NO: 5334).

In some embodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 20 nucleotidefragment of a ribonucleic acid sequence of any of FIGS. 1-15. In someembodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 20 nucleotidefragment of a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of a ribonucleic acid sequence of anyof FIGS. 1-15. In some embodiments, the ribonucleic acid sequence of theat least one ribonucleic acid described above comprises at least a 20nucleotide fragment of a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In some embodiments, theribonucleic acid sequence of the at least one ribonucleic acid describedabove comprises at least a 20 nucleotide fragment of a sequence with asingle nucleotide mismatch to a ribonucleic acid sequence ofGTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). For example, if the targetsequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleicacid sequence of the at least one ribonucleic acid which comprises atleast a 20 nucleotide fragment is GATGCTCAGTACAGCCACCT (SEQ ID NO:5324).

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence selected from the group consisting of at least oneribonucleic acid sequence of FIG. 1 and at least one ribonucleic acidsequence with a single nucleotide mismatch to a ribonucleic acidsequence of FIG. 1, and combinations thereof.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence selected from the group consisting of at least oneribonucleic acid sequence of FIG. 2 and at least one ribonucleic acidsequence with a single nucleotide mismatch to a ribonucleic acidsequence of FIG. 2, and combinations thereof.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence selected from the group consisting of at least oneribonucleic acid sequence of FIG. 3 and at least one ribonucleic acidsequence with a single nucleotide mismatch to a ribonucleic acidsequence of FIG. 3, and combinations thereof.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence selected from the group consisting of at least oneribonucleic acid sequence of FIG. 4 and at least one ribonucleic acidsequence with a single nucleotide mismatch to a ribonucleic acidsequence of FIG. 4, and combinations thereof.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence selected from the group consisting of at least oneribonucleic acid sequence of FIG. 5 and at least one ribonucleic acidsequence with a single nucleotide mismatch to a ribonucleic acidsequence of FIG. 5, and combinations thereof.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence selected from the group consisting of at least oneribonucleic acid sequence of FIG. 6 and at least one ribonucleic acidsequence with a single nucleotide mismatch to a ribonucleic acidsequence of FIG. 6, and combinations thereof.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence selected from the group consisting of at least oneribonucleic acid sequence of FIG. 7 and at least one ribonucleic acidsequence with a single nucleotide mismatch to a ribonucleic acidsequence of FIG. 7, and combinations thereof.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence selected from the group consisting of at least oneribonucleic acid sequence of FIG. 8 and at least one ribonucleic acidsequence with a single nucleotide mismatch to a ribonucleic acidsequence of FIG. 8, and combinations thereof.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence selected from the group consisting of at least oneribonucleic acid sequence of FIG. 9 and at least one ribonucleic acidsequence with a single nucleotide mismatch to a ribonucleic acidsequence of FIG. 9, and combinations thereof.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence selected from the group consisting of at least oneribonucleic acid sequence of FIG. 10 and at least one ribonucleic acidsequence with a single nucleotide mismatch to a ribonucleic acidsequence of FIG. 10, and combinations thereof.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence selected from the group consisting of at least oneribonucleic acid sequence of FIG. 11 and at least one ribonucleic acidsequence with a single nucleotide mismatch to a ribonucleic acidsequence of FIG. 11, and combinations thereof.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence selected from the group consisting of at least oneribonucleic acid sequence of FIG. 12 and at least one ribonucleic acidsequence with a single nucleotide mismatch to a ribonucleic acidsequence of FIG. 12, and combinations thereof.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence selected from the group consisting of at least oneribonucleic acid sequence of FIG. 13 and at least one ribonucleic acidsequence with a single nucleotide mismatch to a ribonucleic acidsequence of FIG. 13, and combinations thereof.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence selected from the group consisting of at least oneribonucleic acid sequence of FIG. 14 and at least one ribonucleic acidsequence with a single nucleotide mismatch to a ribonucleic acidsequence of FIG. 14, and combinations thereof.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence selected from the group consisting of at least oneribonucleic acid sequence of FIG. 15 and at least one ribonucleic acidsequence with a single nucleotide mismatch to a ribonucleic acidsequence of FIG. 15, and combinations thereof.

In some aspects, the present invention comprises a kit for altering atarget polynucleotide sequence in a cell comprising a Cas9 protein or anucleic acid encoding the Cas9 protein, and at least one ribonucleicacid sequence selected from the group consisting of at least oneribonucleic acid sequence of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321)and at least one ribonucleic acid sequence with a single nucleotidemismatch to a ribonucleic acid sequence of GTAACGGCAGACTTCTCCACAGG (SEQID NO: 5321).

In some embodiments, the at least one ribonucleic acid sequencesdescribed above do not include the 3 nucleotide NGG sequence. Forexample, if the target site sequence is GATGCTCAGTACAGCCACCTTGG (SEQ IDNO: 5323), the ribonucleic acid sequence of the at least one ribonucleicacid sequence is GATGCTCAGTACAGCCACCT (SEQ ID NO: 5324). As anotherexample, if the target sequence is GATGCTCAGTACAGCCACCTTGG (SEQ ID NO:5323), a ribonucleic acid sequence with a single nucleotide mismatchwhich does not include the 3 nucleotide NGG sequence isGATGCTGAGTACAGCCACCT (SEQ ID NO: 5326), with the italicized G being themismatched nucleotide. Those skilled in the art will appreciate,however, that the single nucleotide mismatch can comprise any nucleotidein the ribonucleic acid, e.g., the first nucleotide, the secondnucleotide, the third nucleotide, the fourth nucleotide, the fifthnucleotide, the sixth nucleotide, the seventh nucleotide, the eighthnucleotide, the ninth nucleotide, the tenth nucleotide, the eleventhnucleotide, the twelfth nucleotide, the thirteenth nucleotide, thefourteenth nucleotide, the fifteenth nucleotide, the sixteenthnucleotide, the seventeenth nucleotide, the eighteenth nucleotide, thenineteenth nucleotide, or the twentieth nucleotide of the ribonucleicacid.

In some embodiments, the at least one ribonucleic acid described abovecomprises at least a 12 nucleotide fragment of a ribonucleic acidsequence of any of FIGS. 1-15. In some embodiments, the at least oneribonucleic acid described above comprises at least a 12 nucleotidefragment of a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of a ribonucleic acid sequence of anyof FIGS. 1-15 For example, if the target sequence isGATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleic acid sequenceof the at least one ribonucleic acid which comprises at least a 12nucleotide fragment is GTACAGCCACCT (SEQ ID NO: 5327).

In some embodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 13 nucleotidefragment of a ribonucleic acid sequence of any of FIGS. 1-15. In someembodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 13 nucleotidefragment of a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of a ribonucleic acid sequence of anyof FIGS. 1-15. For example, if the target sequence isGATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleic acid sequenceof the at least one ribonucleic acid which comprises at least a 13nucleotide fragment is AGTACAGCCACCT (SEQ ID NO: 5328).

In some embodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 14 nucleotidefragment of a ribonucleic acid sequence of any of FIGS. 1-15. In someembodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 14 nucleotidefragment of a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of a ribonucleic acid sequence of anyof FIGS. 1-15. For example, if the target sequence isGATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleic acid sequenceof the at least one ribonucleic acid which comprises at least a 14nucleotide fragment is CAGTACAGCCACCT (SEQ ID NO: 5329).

In some embodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 15 nucleotidefragment of a ribonucleic acid sequence of any of FIGS. 1-15. In someembodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 15 nucleotidefragment of a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of a ribonucleic acid sequence of anyof FIGS. 1-15. For example, if the target sequence isGATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleic acid sequenceof the at least one ribonucleic acid which comprises at least a 15nucleotide fragment is TCAGTACAGCCACCT (SEQ ID NO: 5330).

In some embodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprise at least a 16 nucleotidefragment of a ribonucleic acid sequence of any of FIGS. 1-15. In someembodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 16 nucleotidefragment of a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of a ribonucleic acid sequence of anyof FIGS. 1-15. For example, if the target sequence isGATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleic acid sequenceof the at least one ribonucleic acid which comprises at least a 16nucleotide fragment is CTCAGTACAGCCACCT (SEQ ID NO: 5331).

In some embodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 17 nucleotidefragment of a ribonucleic acid sequence of any of FIGS. 1-15. In someembodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 17 nucleotidefragment of a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of a ribonucleic acid sequence of anyof FIGS. 1-15. For example, if the target sequence isGATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleic acid sequenceof the at least one ribonucleic acid which comprises at least a 17nucleotide fragment is GCTCAGTACAGCCACCT (SEQ ID NO: 5332).

In some embodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 18 nucleotidefragment of a ribonucleic acid sequence of any of FIGS. 1-15. In someembodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 18 nucleotidefragment of a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of a ribonucleic acid sequence of anyof FIGS. 1-15. For example, if the target sequence isGATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleic acid sequenceof the at least one ribonucleic acid which comprises at least a 18nucleotide fragment is TGCTCAGTACAGCCACCT (SEQ ID NO: 5333).

In some embodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprise at least a 19 nucleotidefragment of a ribonucleic acid sequence of any of FIGS. 1-15. In someembodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 19 nucleotidefragment of a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of a ribonucleic acid sequence of anyof FIGS. 1-15. For example, if the target sequence isGATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleic acid sequenceof the at least one ribonucleic acid which comprises at least a 19nucleotide fragment is ATGCTCAGTACAGCCACCT (SEQ ID NO: 5334).

In some embodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 20 nucleotidefragment of a ribonucleic acid sequence of any of FIGS. 1-15. In someembodiments, the ribonucleic acid sequence of the at least oneribonucleic acid described above comprises at least a 20 nucleotidefragment of a sequence with a single nucleotide mismatch to a sequenceselected from the group consisting of a ribonucleic acid sequence of anyof FIGS. 1-15. For example, if the target sequence isGATGCTCAGTACAGCCACCTTGG (SEQ ID NO: 5323), the ribonucleic acid sequenceof the at least one ribonucleic acid which comprises at least a 20nucleotide fragment is GATGCTCAGTACAGCCACCT (SEQ ID NO: 5324).

In some embodiments, the at least one ribonucleic acid described abovecomprises at least a 12 nucleotide fragment, at least a 13 nucleotidefragment, at least a 14 nucleotide fragment, at least a 15 nucleotidefragment, at least a 16 nucleotide fragment, at least a 17 nucleotidefragment, at least an 18 nucleotide fragment, at least a 19 nucleotidefragment, or at least a 20 nucleotide sequence of a ribonucleic acidsequence of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321). In someembodiments, the at least one ribonucleic acid described above comprisesat least a 12, at least a 13, at least a 14, at least a 15, at least a,at least a 17, at least an 18, at least a 19, or at least a 20nucleotide fragment of a sequence with a single nucleotide mismatch to aribonucleic acid sequence of GTAACGGCAGACTTCTCCACAGG (SEQ ID NO: 5321).

In some embodiments, the kit comprises one or more cell lines, cultures,or populations selected from the group consisting of human pluripotentcells, primary human cells, and non-transformed cells. In someembodiments, the kit comprises a DNA repair template.

In some embodiments, the DNA repair template comprises one or morenormal or wild-type ADA gene sequences. In some embodiments, the DNArepair template comprises one or more normal or wild-type DNA sequencesthat correspond to mutant ADA sequences to be cleaved from targetSCID-associated polynucleotide sequences.

In some embodiments, the DNA repair template comprises one or morenormal or wild-type AK2 gene sequences. In some embodiments, the DNArepair template comprises one or more normal or wild-type DNA sequencesthat correspond to mutant AK2 sequences to be cleaved from targetSCID-associated polynucleotide sequences.

In some embodiments, the DNA repair template comprises one or morenormal or wild-type CD3D gene sequences. In some embodiments, the DNArepair template comprises one or more normal or wild-type DNA sequencesthat correspond to mutant CD3D sequences to be cleaved from targetSCID-associated polynucleotide sequences.

In some embodiments, the DNA repair template comprises one or morenormal or wild-type DCLRE1C gene sequences. In some embodiments, the DNArepair template comprises one or more normal or wild-type DNA sequencesthat correspond to mutant DCLRE1C sequences to be cleaved from targetSCID-associated polynucleotide sequences.

In some embodiments, the DNA repair template comprises one or morenormal or wild-type IL2RG gene sequences. In some embodiments, the DNArepair template comprises one or more normal or wild-type DNA sequencesthat correspond to mutant IL2RG sequences to be cleaved from targetSCID-associated polynucleotide sequences.

In some embodiments, the DNA repair template comprises one or morenormal or wild-type IL7R gene sequences. In some embodiments, the DNArepair template comprises one or more normal or wild-type DNA sequencesthat correspond to mutant IL7R sequences to be cleaved from targetSCID-associated polynucleotide sequences.

In some embodiments, the DNA repair template comprises one or morenormal or wild-type JAK3 gene sequences. In some embodiments, the DNArepair template comprises one or more normal or wild-type DNA sequencesthat correspond to mutant JAK3 sequences to be cleaved from targetSCID-associated polynucleotide sequences.

In some embodiments, the DNA repair template comprises one or morenormal or wild-type NHEJ1 gene sequences. In some embodiments, the DNArepair template comprises one or more normal or wild-type DNA sequencesthat correspond to mutant NHEJ1 sequences to be cleaved from targetSCID-associated polynucleotide sequences.

In some embodiments, the DNA repair template comprises one or morenormal or wild-type PNP gene sequences. In some embodiments, the DNArepair template comprises one or more normal or wild-type DNA sequencesthat correspond to mutant PNP sequences to be cleaved from targetSCID-associated polynucleotide sequences.

In some embodiments, the DNA repair template comprises one or morenormal or wild-type PRKDC gene sequences. In some embodiments, the DNArepair template comprises one or more normal or wild-type DNA sequencesthat correspond to mutant PRKDC sequences to be cleaved from targetSCID-associated polynucleotide sequences.

In some embodiments, the DNA repair template comprises one or morenormal or wild-type RAG1 gene sequences. In some embodiments, the DNArepair template comprises one or more normal or wild-type DNA sequencesthat correspond to mutant RAG1 sequences to be cleaved from targetSCID-associated polynucleotide sequences.

In some embodiments, the DNA repair template comprises one or morenormal or wild-type RAG2 gene sequences. In some embodiments, the DNArepair template comprises one or more normal or wild-type DNA sequencesthat correspond to mutant RAG2 sequences to be cleaved from targetSCID-associated polynucleotide sequences.

In some embodiments, the DNA repair template comprises one or morenormal or wild-type ZAP70 gene sequences. In some embodiments, the DNArepair template comprises one or more normal or wild-type DNA sequencesthat correspond to mutant ZAP70 sequences to be cleaved from targetSCID-associated polynucleotide sequences.

In some embodiments, the DNA repair template comprises one or morenormal or wild-type HBB gene sequences. In some embodiments, the DNArepair template comprises one or more normal or wild-type DNA sequencesthat correspond to mutant HBB sequences to be cleaved from targetSCD-associated polynucleotide sequences.

In some embodiments, the DNA repair template comprises one or morenormal or wild-type DNA sequences that correspond to mutant HBBsequences to be cleaved from target beta thalassemia-associatedpolynucleotide sequences.

It should be appreciated that the methods, compositions, and kits of thepresent invention may employ nanoparticles or lipid nanoparticles as avehicle for delivering, or introducing a Cas protein and/or aribonucleic acid of the present invention into a cell.

In some embodiments, the lipid nanoparticle comprises at least one of acationic lipid, a neutral lipid, an amino lipid, a sterol, and a PEG orPEG-modified lipid.

The cationic lipid may be, for example, N,N-dioleyl-N,N-dimethylammoniumchloride (DODAC), N,N-distearyl-N,N-dimethylammonium bromide (DDAB),N—(I-(2,3-dioleoyloxy)propyl)-N,N,N-trimethylammonium chloride (DOTAP),N—(I-(2,3-dioleyloxy)propyl)-N,N,N-trimethylammonium chloride (DOTMA),N,N-dimethyl-2,3-dioleyloxy)propylamine (DODMA),1,2-DiLinoleyloxy-N,N-dimethylaminopropane (DLinDMA),1,2-Dilinolenyloxy-N,N-dimethylaminopropane (DLenDMA),1,2-Dilinoleylcarbamoyloxy-3-dimethylaminopropane (DLin-C-DAP),1,2-Dilinoleyoxy-3-(dimethylamino)acetoxypropane (DLin-DAC),1,2-Dilinoleyoxy-3-morpholinopropane (DLin-MA),1,2-Dilinoleoyl-3-dimethylaminopropane (DLinDAP),1,2-Dilinoleylthio-3-dimethylaminopropane (DLin-S-DMA),1-Linoleoyl-2-linoleyloxy-3-dimethylaminopropane (DLin-2-DMAP),1,2-Dilinoleyloxy-3-trimethylaminopropane chloride salt (DLin-TMA.C1),1,2-Dilinoleoyl-3-trimethylaminopropane chloride salt (DLin-TAP.C1),1,2-Dilinoleyloxy-3-(N-methylpiperazino)propane (DLin-MPZ), or3-(N,N-Dilinoleylamino)-1,2-propanediol (DLinAP),3-(N,N-Dioleylamino)-1,2-propanedio (DOAP),1,2-Dilinoleyloxo-3-(2-N,N-dimethylamino)ethoxypropane (DLin-EG-DMA),1,2-Dilinolenyloxy-N,N-dimethylaminopropane (DLinDMA),2,2-Dilinoleyl-4-dimethylaminomethyl-[1,3]-dioxolane (DLin-K-DMA) oranalogs thereof,(3aR,5s,6aS)-N,N-dimethyl-2,2-di((9Z,12Z)-octadeca-9,12-dienyl)tetrahydro-3aH-cyclopenta[d][1,3]dioxol-5-amine(ALNY-100), (6Z,9Z,28Z,31Z)-heptatriaconta-6,9,28,31-tetraen-19-yl4-(dimethylamino)butanoate (MC3), or a mixture thereof.

Other cationic lipids, which carry a net positive charge at aboutphysiological pH, in addition to those specifically described above, mayalso be included in lipid particles of the invention. Such cationiclipids include, but are not limited to, N,N-dioleyl-N,N-dimethylammoniumchloride (“DODAC”); N-(2,3-dioleyloxy)propyl-N,N—N-triethylammoniumchloride (“DOTMA”); N,N-distearyl-N,N-dimethylammonium bromide (“DDAB”);N-(2,3-dioleoyloxy)propyl)-N,N,N-trimethylammonium chloride (“DOTAP”);1,2-Dioleyloxy-3-trimethylaminopropane chloride salt (“DOTAP.Cl”);3.beta.-(N—(N′,N′-dimethylaminoethane)-carbamoyl)cholesterol(“DC-Chol”),N-(1-(2,3-dioleyloxy)propyl)-N-2-(sperminecarboxamido)ethyl)-N,N-dimethyl-ammoniumtrifluoracetate (“DOSPA”), dioctadecylamidoglycyl carboxyspermine(“DOGS”), 1,2-dileoyl-sn-3-phosphoethanolamine (“DOPE”),1,2-dioleoyl-3-dimethylammonium propane (“DODAP”),N,N-dimethyl-2,3-dioleyloxy)propylamine (“DODMA”), andN-(1,2-dimyristyloxyprop-3-yl)-N,N-dimethyl-N-hydroxyethyl ammoniumbromide (“DMRIE”), and mixtures thereof. Additionally, a number ofcommercial preparations of cationic lipids can be used, such as, e.g.,LIPOFECTIN (including DOTMA and DOPE, available from GIBCO/BRL), andLIPOFECTAMINE (comprising DOSPA and DOPE, available from GIBCO/BRL). Inparticular embodiments, a cationic lipid is an amino lipid.

As used herein, the term “amino lipid” is meant to include those lipidshaving one or two fatty acid or fatty alkyl chains and an amino headgroup (including an alkylamino or dialkylamino group) that may beprotonated to form a cationic lipid at physiological pH.

Other amino lipids would include those having alternative fatty acidgroups and other dialkylamino groups, including those in which the alkylsubstituents are different (e.g., N-ethyl-N-methylamino-,N-propyl-N-ethylamino- and the like). For those embodiments in which R¹¹and R¹² are both long chain alkyl or acyl groups, they can be the sameor different. In general, amino lipids having less saturated acyl chainsare more easily sized, particularly when the complexes must be sizedbelow about 0.3 microns, for purposes of filter sterilization. Aminolipids containing unsaturated fatty acids with carbon chain lengths inthe range of C₁₄ to C₂₂ are preferred. Other scaffolds can also be usedto separate the amino group and the fatty acid or fatty alkyl portion ofthe amino lipid. Suitable scaffolds are known to those of skill in theart.

Specific examples of PEG-modified lipids (or lipid-polyoxyethyleneconjugates) that are useful in the present invention can have a varietyof “anchoring” lipid portions to secure the PEG portion to the surfaceof the lipid vesicle. Examples of suitable PEG-modified lipids includePEG-modified phosphatidylethanolamine and phosphatidic acid,PEG-ceramide conjugates (e.g., PEG-CerC14 or PEG-CerC20) which aredescribed in U.S. Pat. No. 5,820,873, incorporated herein by reference,PEG-modified dialkylamines and PEG-modified1,2-diacyloxypropan-3-amines. Particularly preferred are PEG-modifieddiacylglycerols and dialkylglycerols.

Examples of suitable neutral lipid include DPSC, DPPC, POPC, DOPE, SM,and mixtures thereof.

As used herein “nucleic acid,” in its broadest sense, includes anycompound and/or substance that comprise a polymer of nucleotides linkedvia a phosphodiester bond. Exemplary nucleic acids include ribonucleicacids (RNAs), deoxyribonucleic acids (DNAs), threose nucleic acids(TNAs), glycol nucleic acids (GNAs), peptide nucleic acids (PNAs),locked nucleic acids (LNAs) or hybrids thereof. They may also includeRNAi-inducing agents, RNAi agents, siRNAs, shRNAs, miRNAs, antisenseRNAs, ribozymes, catalytic DNA, tRNA, RNAs that induce triple helixformation, aptamers, vectors, etc. In some embodiments, the nucleic acidencoding the Cas protein is an mRNA. In some embodiments, the Casprotein is encoded by a modified nucleic acid (e.g., a synthetic,modified mRNA described herein).

The present invention contemplates the use of any nucleic acidmodification available to the skilled artisan. The nucleic acids of thepresent invention can include any number of modifications. In someembodiments, the nucleic acid comprises one or more modificationsselected from the group consisting of pyridin-4-one ribonucleoside,5-aza-uridine, 2-thio-5-aza-uridine, 2-thiouridine,4-thio-pseudouridine, 2-thio-pseudouridine, 5-hydroxyuridine,3-methyluridine, 5-carboxymethyl-uridine, 1-carboxymethyl-pseudouridine,5-propynyl-uridine, 1-propynyl-pseudouridine, 5-taurinomethyluridine,1-taurinomethyl-pseudouridine, 5-taurinomethyl-2-thio-uridine,1-taurinomethyl-4-thio-uridine, 5-methyl-uridine,1-methyl-pseudouridine, 4-thio-1-methyl-pseudouridine,2-thio-1-methyl-pseudouridine, 1-methyl-1-deaza-pseudouridine,2-thio-1-methyl-1-deaza-pseudouridine, dihydrouridine,dihydropseudouridine, 2-thio-dihydrouridine,2-thio-dihydropseudouridine, 2-methoxyuridine, 2-methoxy-4-thio-uridine,4-methoxy-pseudouridine, 4-methoxy-2-thio-pseudouridine, 5-aza-cytidine,pseudoisocytidine, 3-methyl-cytidine, N4-acetylcytidine,5-formylcytidine, N4-methylcytidine, 5-hydroxymethylcytidine,1-methyl-pseudoisocytidine, pyrrolo-cytidine, pyrrolo-pseudoisocytidine,2-thio-cytidine, 2-thio-5-methyl-cytidine, 4-thio-pseudoisocytidine,4-thio-1-methyl-pseudoisocytidine,4-thio-1-methyl-1-deaza-pseudoisocytidine,1-methyl-1-deaza-pseudoisocytidine, zebularine, 5-aza-zebularine,5-methyl-zebularine, 5-aza-2-thio-zebularine, 2-thio-zebularine,2-methoxy-cytidine, 2-methoxy-5-methyl-cytidine,4-methoxy-pseudoisocytidine, 4-methoxy-1-methyl-pseudoisocytidine,2-aminopurine, 2,6-diaminopurine, 7-deaza-adenine,7-deaza-8-aza-adenine, 7-deaza-2-aminopurine,7-deaza-8-aza-2-aminopurine, 7-deaza-2,6-diaminopurine,7-deaza-8-aza-2,6-diaminopurine, 1-methyladenosine, N6-methyladenosine,N6-isopentenyladenosine, N6-(cis-hydroxyisopentenyl)adenosine,2-methylthio-N6-(cis-hydroxyisopentenyl)adenosine,N6-glycinylcarbamoyladenosine, N6-threonylcarbamoyladenosine,2-methylthio-N6-threonyl carbamoyladenosine, N6,N6-dimethyladenosine,7-methyladenine, 2-methylthio-adenine, and 2-methoxy-adenine, inosine,1-methyl-inosine, wyosine, wybutosine, 7-deaza-guanosine,7-deaza-8-aza-guanosine, 6-thio-guanosine, 6-thio-7-deaza-guanosine,6-thio-7-deaza-8-aza-guanosine, 7-methyl-guanosine,6-thio-7-methyl-guanosine, 7-methylinosine, 6-methoxy-guanosine,1-methylguanosine, N2-methylguanosine, N2,N2-dimethylguanosine,8-oxo-guanosine, 7-methyl-8-oxo-guanosine, 1-methyl-6-thio-guanosine,N2-methyl-6-thio-guanosine, and N2,N2-dimethyl-6-thio-guanosine, andcombinations thereof.

Preparation of modified nucleosides and nucleotides used in themanufacture or synthesis of modified RNAs of the present invention caninvolve the protection and deprotection of various chemical groups. Theneed for protection and deprotection, and the selection of appropriateprotecting groups can be readily determined by one skilled in the art.

The chemistry of protecting groups can be found, for example, in Greene,et al., Protective Groups in Organic Synthesis, 2d. Ed., Wiley & Sons,1991, which is incorporated herein by reference in its entirety.

Modified nucleosides and nucleotides can be prepared according to thesynthetic methods described in Ogata et al. Journal of Organic Chemistry74:2585-2588, 2009; Purmal et al. Nucleic Acids Research 22(1): 72-78,1994; Fukuhara et al. Biochemistry 1(4): 563-568, 1962; and Xu et al.Tetrahedron 48(9): 1729-1740, 1992, each of which are incorporated byreference in their entirety.

Modified nucleic acids (e.g., ribonucleic acids) need not be uniformlymodified along the entire length of the molecule. Different nucleotidemodifications and/or backbone structures may exist at various positionsin the nucleic acid. One of ordinary skill in the art will appreciatethat the nucleotide analogs or other modification(s) may be located atany position(s) of a nucleic acid such that the function of the nucleicacid is not substantially decreased. A modification may also be a 5′ or3′ terminal modification. The nucleic acids may contain at a minimum oneand at maximum 100% modified nucleotides, or any intervening percentage,such as at least 50% modified nucleotides, at least 80% modifiednucleotides, or at least 90% modified nucleotides.

In some embodiments, at least one of the one to two ribonucleic acids isa modified ribonucleic acid. In some embodiments, each of the one to tworibonucleic acids is a modified ribonucleic acid. In some embodiments,at least one of the multiple ribonucleic acids is a modified ribonucleicacid. In some embodiments, a plurality of the multiple ribonucleic acidsare modified. In some embodiments, each of the multiple ribonucleicacids are modified. Those skilled in the art will appreciate that themodified ribonucleic acids can include one or more of the nucleic acidmodification described herein.

In some aspects, provided herein are synthetic, modified RNA moleculesencoding polypeptides, where the synthetic, modified RNA moleculescomprise one or more modifications, such that introducing the synthetic,modified RNA molecules to a cell results in a reduced innate immuneresponse relative to a cell contacted with synthetic RNA moleculesencoding the polypeptides not comprising the one or more modifications.In some embodiments, the Cas protein comprises a synthetic, modified RNAmolecule encoding a Cas protein. In some embodiments, the Cas proteincomprises a synthetic, modified RNA molecule encoding a Cas9 protein.

The synthetic, modified RNAs described herein include modifications toprevent rapid degradation by endo- and exo-nucleases and to avoid orreduce the cell's innate immune or interferon response to the RNA.Modifications include, but are not limited to, for example, (a) endmodifications, e.g., 5′ end modifications (phosphorylationdephosphorylation, conjugation, inverted linkages, etc.), 3′ endmodifications (conjugation, DNA nucleotides, inverted linkages, etc.),(b) base modifications, e.g., replacement with modified bases,stabilizing bases, destabilizing bases, or bases that base pair with anexpanded repertoire of partners, or conjugated bases, (c) sugarmodifications (e.g., at the 2′ position or 4′ position) or replacementof the sugar, as well as (d) internucleoside linkage modifications,including modification or replacement of the phosphodiester linkages. Tothe extent that such modifications interfere with translation (i.e.,results in a reduction of 50% or more in translation relative to thelack of the modification—e.g., in a rabbit reticulocyte in vitrotranslation assay), the modification is not suitable for the methods andcompositions described herein. Specific examples of synthetic, modifiedRNA compositions useful with the methods described herein include, butare not limited to, RNA molecules containing modified or non-naturalinternucleoside linkages. Synthetic, modified RNAs having modifiedinternucleoside linkages include, among others, those that do not have aphosphorus atom in the internucleoside linkage. In other embodiments,the synthetic, modified RNA has a phosphorus atom in its internucleosidelinkage(s).

Non-limiting examples of modified internucleoside linkages includephosphorothioates, chiral phosphorothioates, phosphorodithioates,phosphotriesters, aminoalkylphosphotriesters, methyl and other alkylphosphonates including 3′-alkylene phosphonates and chiral phosphonates,phosphinates, phosphoramidates including 3′-amino phosphoramidate andaminoalkylphosphoramidates, thionophosphoramidates,thionoalkylphosphonates, thionoalkylphosphotriesters, andboranophosphates having normal 3′-5′ linkages, 2′-5′ linked analogs ofthese, and those) having inverted polarity wherein the adjacent pairs ofnucleoside units are linked 3′-5′ to 5′-3′ or 2′-5′ to 5′-2′. Varioussalts, mixed salts and free acid forms are also included.

Representative U.S. patents that teach the preparation of the abovephosphorus-containing linkages include, but are not limited to, U.S.Pat. Nos. 3,687,808; 4,469,863; 4,476,301; 5,023,243; 5,177,195;5,188,897; 5,264,423; 5,276,019; 5,278,302; 5,286,717; 5,321,131;5,399,676; 5,405,939; 5,453,496; 5,455,233; 5,466,677; 5,476,925;5,519,126; 5,536,821; 5,541,316; 5,550,111; 5,563,253; 5,571,799;5,587,361; 5,625,050; 6,028,188; 6,124,445; 6,160,109; 6,169,170;6,172,209; 6,239,265; 6,277,603; 6,326,199; 6,346,614; 6,444,423;6,531,590; 6,534,639; 6,608,035; 6,683,167; 6,858,715; 6,867,294;6,878,805; 7,015,315; 7,041,816; 7,273,933; 7,321,029; and U.S. Pat. RE39464, each of which is herein incorporated by reference in itsentirety.

Modified internucleoside linkages that do not include a phosphorus atomtherein have internucleoside linkages that are formed by short chainalkyl or cycloalkyl internucleoside linkages, mixed heteroatoms andalkyl or cycloalkyl internucleoside linkages, or one or more short chainheteroatomic or heterocyclic internucleoside linkages. These includethose having morpholino linkages (formed in part from the sugar portionof a nucleoside); siloxane backbones; sulfide, sulfoxide and sulfonebackbones; formacetyl and thioformacetyl backbones; methylene formacetyland thioformacetyl backbones; alkene containing backbones; sulfamatebackbones; methyleneimino and methylenehydrazino backbones; sulfonateand sulfonamide backbones; amide backbones; and others having mixed N,O, S and CH2 component parts.

Representative U.S. patents that teach the preparation of modifiedoligonucleosides include, but are not limited to, U.S. Pat. Nos.5,034,506; 5,166,315; 5,185,444; 5,214,134; 5,216,141; 5,235,033;5,64,562; 5,264,564; 5,405,938; 5,434,257; 5,466,677; 5,470,967;5,489,677; 5,541,307; 5,561,225; 5,596,086; 5,602,240; 5,608,046;5,610,289; 5,618,704; 5,623,070; 5,663,312; 5,633,360; 5,677,437; and5,677,439, each of which is herein incorporated by reference in itsentirety.

Some embodiments of the synthetic, modified RNAs described hereininclude nucleic acids with phosphorothioate internucleoside linkages andoligonucleosides with heteroatom internucleoside linkage, and inparticular —CH2-NH—CH2-, —CH2-N(CH3)-O—CH2-[known as a methylene(methylimino) or MMI], —CH2-O—N(CH3)-CH2-, —CH2-N(CH3)-N(CH3)-CH2- and—N(CH3)-CH2-CH2-[wherein the native phosphodiester internucleosidelinkage is represented as —O—P—O—CH2-] of the above-referenced U.S. Pat.No. 5,489,677, and the amide backbones of the above-referenced U.S. Pat.No. 5,602,240, both of which are herein incorporated by reference intheir entirety. In some embodiments, the nucleic acid sequences featuredherein have morpholino backbone structures of the above-referenced U.S.Pat. No. 5,034,506, herein incorporated by reference in its entirety.

Synthetic, modified RNAs described herein can also contain one or moresubstituted sugar moieties. The nucleic acids featured herein caninclude one of the following at the 2′ position: H (deoxyribose); OH(ribose); F; O-, S-, or N-alkyl; O-, S-, or N-alkenyl; O-, S- orN-alkynyl; or O-alkyl-O-alkyl, wherein the alkyl, alkenyl and alkynylcan be substituted or unsubstituted C1 to C10 alkyl or C2 to C10 alkenyland alkynyl. Exemplary modifications include O[(CH2)nO]mCH3,O(CH2).nOCH3, O(CH2)nNH2, O(CH2)nCH3, O(CH2)nONH2, andO(CH2)nON[(CH2)nCH3)]2, where n and m are from 1 to about 10. In someembodiments, synthetic, modified RNAs include one of the following atthe 2′ position: C1 to C10 lower alkyl, substituted lower alkyl,alkaryl, aralkyl, O-alkaryl or O-aralkyl, SH, SCH3, OCN, Cl, Br, CN,CF3, OCF3, SOCH3, SO2CH3, ONO2, NO2, N3, NH2, heterocycloalkyl,heterocycloalkaryl, aminoalkylamino, polyalkylamino, substituted silyl,a reporter group, an intercalator, a group for improving thepharmacokinetic properties of an RNA, or a group for improving thepharmacodynamic properties of a synthetic, modified RNA, and othersubstituents having similar properties. In some embodiments, themodification includes a 2′ methoxyethoxy (2′-O—CH2CH2OCH3, also known as2′-O-(2-methoxyethyl) or 2′-MOE) (Martin et al., Helv. Chim. Acta, 1995,78:486-504) i.e., an alkoxy-alkoxy group. Another exemplary modificationis 2′-dimethylaminooxyethoxy, i.e., a O(CH2)20N(CH3)2 group, also knownas 2′-DMAOE, and 2′-dimethylaminoethoxyethoxy (also known in the art as2′-O-dimethylaminoethoxyethyl or 2′-DMAEOE), i.e.,2′-O—CH2-O—CH2-N(CH2)2.

Other modifications include 2′-methoxy (2′-OCH3), 2′-aminopropoxy(2′-OCH2CH2CH2NH2) and 2′-fluoro (2′-F). Similar modifications can alsobe made at other positions on the nucleic acid sequence, particularlythe 3′ position of the sugar on the 3′ terminal nucleotide or in 2′-5′linked nucleotides and the 5′ position of 5′ terminal nucleotide. Asynthetic, modified RNA can also have sugar mimetics such as cyclobutylmoieties in place of the pentofuranosyl sugar. Representative U.S.patents that teach the preparation of such modified sugar structuresinclude, but are not limited to, U.S. Pat. Nos. 4,981,957; 5,118,800;5,319,080; 5,359,044; 5,393,878; 5,446,137; 5,466,786; 5,514,785;5,519,134; 5,567,811; 5,576,427; 5,591,722; 5,597,909; 5,610,300;5,627,053; 5,639,873; 5,646,265; 5,658,873; 5,670,633; and 5,700,920,certain of which are commonly owned with the instant application, andeach of which is herein incorporated by reference in its entirety.

As non-limiting examples, synthetic, modified RNAs described herein caninclude at least one modified nucleoside including a 2′-O-methylmodified nucleoside, a nucleoside comprising a 5′ phosphorothioategroup, a 2′-amino-modified nucleoside, 2′-alkyl-modified nucleoside,morpholino nucleoside, a phosphoramidate or a non-natural basecomprising nucleoside, or any combination thereof.

In some embodiments of this aspect and all other such aspects describedherein, the at least one modified nucleoside is selected from the groupconsisting of 5-methylcytidine (5mC), N6-methyladenosine (m6A),3,2′-O-dimethyluridine (m4U), 2-thiouridine (s2U), 2′ fluorouridine,pseudouridine, 2′-O-methyluridine (Um), 2′ deoxyuridine (2′ dU),4-thiouridine (s4U), 5-methyluridine (m5U), 2′-O-methyladenosine (m6A),N6,2′-O-dimethyladenosine (m6Am), N6,N6,2′-O-trimethyladenosine (m62Am),2′-O-methylcytidine (Cm), 7-methylguanosine (m7G), 2′-O-methylguanosine(Gm), N2,7-dimethylguanosine (m2,7G), N2,N2,7-trimethylguanosine(m2,2,7G), and inosine (I).

Alternatively, a synthetic, modified RNA can comprise at least twomodified nucleosides, at least 3, at least 4, at least 5, at least 6, atleast 7, at least 8, at least 9, at least 10, at least 15, at least 20or more, up to the entire length of the nucleotide. At a minimum, asynthetic, modified RNA molecule comprising at least one modifiednucleoside comprises a single nucleoside with a modification asdescribed herein. It is not necessary for all positions in a givensynthetic, modified RNA to be uniformly modified, and in fact more thanone of the aforementioned modifications can be incorporated in a singlesynthetic, modified RNA or even at a single nucleoside within asynthetic, modified RNA. However, it is preferred, but not absolutelynecessary, that each occurrence of a given nucleoside in a molecule ismodified (e.g., each cytosine is a modified cytosine e.g., 5mC).However, it is also contemplated that different occurrences of the samenucleoside can be modified in a different way in a given synthetic,modified RNA molecule (e.g., some cytosines modified as 5mC, othersmodified as 2′-O-methylcytidine or other cytosine analog). Themodifications need not be the same for each of a plurality of modifiednucleosides in a synthetic, modified RNA. Furthermore, in someembodiments of the aspects described herein, a synthetic, modified RNAcomprises at least two different modified nucleosides. In some suchpreferred embodiments of the aspects described herein, the at least twodifferent modified nucleosides are 5-methylcytidine and pseudouridine. Asynthetic, modified RNA can also contain a mixture of both modified andunmodified nucleosides.

As used herein, “unmodified” or “natural” nucleosides or nucleobasesinclude the purine bases adenine (A) and guanine (G), and the pyrimidinebases thymine (T), cytosine (C) and uracil (U). In some embodiments, asynthetic, modified RNA comprises at least one nucleoside (“base”)modification or substitution. Modified nucleosides include othersynthetic and natural nucleobases such as inosine, xanthine,hypoxanthine, nubularine, isoguanisine, tubercidine, 2-(halo)adenine,2-(alkyl)adenine, 2-(propyl)adenine, 2 (amino)adenine,2-(aminoalkyl)adenine, 2 (aminopropyl)adenine, 2 (methylthio) N6(isopentenyl)adenine, 6 (alkyl)adenine, 6 (methyl)adenine, 7(deaza)adenine, 8 (alkenyl)adenine, 8-(alkyl)adenine, 8(alkynyl)adenine, 8 (amino)adenine, 8-(halo)adenine,8-(hydroxyl)adenine, 8 (thioalkyl)adenine, 8-(thiol)adenine,N6-(isopentyl)adenine, N6 (methyl)adenine, N6, N6 (dimethyl)adenine,2-(alkyl)guanine, 2 (propyl)guanine, 6-(alkyl)guanine, 6(methyl)guanine, 7 (alkyl)guanine, 7 (methyl)guanine, 7 (deaza)guanine,8 (alkyl)guanine, 8-(alkenyl)guanine, 8 (alkynyl)guanine,8-(amino)guanine, 8 (halo)guanine, 8-(hydroxyl)guanine, 8(thioalkyl)guanine, 8-(thiol)guanine, N (methyl)guanine,2-(thio)cytosine, 3 (deaza) 5 (aza)cytosine, 3-(alkyl)cytosine, 3(methyl)cytosine, 5-(alkyl)cytosine, 5-(alkynyl)cytosine, 5(halo)cytosine, 5 (methyl)cytosine, 5 (propynyl)cytosine, 5(propynyl)cytosine, 5 (trifluoromethyl)cytosine, 6-(azo)cytosine, N4(acetyl)cytosine, 3 (3 amino-3 carboxypropyl)uracil, 2-(thio)uracil, 5(methyl) 2 (thio)uracil, 5 (methylaminomethyl)-2 (thio)uracil,4-(thio)uracil, 5 (methyl) 4 (thio)uracil, 5 (methylaminomethyl)-4(thio)uracil, 5 (methyl) 2,4 (dithio)uracil, 5 (methylaminomethyl)-2,4(dithio)uracil, 5 (2-aminopropyl)uracil, 5-(alkyl)uracil,5-(alkynyl)uracil, 5-(allylamino)uracil, 5 (aminoallyl)uracil, 5(aminoalkyl)uracil, 5 (guanidiniumalkyl)uracil, 5(1,3-diazole-1-alkyl)uracil, 5-(cyanoalkyl)uracil,5-(dialkylaminoalkyl)uracil, 5 (dimethylaminoalkyl)uracil,5-(halo)uracil, 5-(methoxy)uracil, uracil-5 oxyacetic acid, 5(methoxycarbonylmethyl)-2-(thio)uracil, 5(methoxycarbonyl-methyl)uracil, 5 (propynyl)uracil, 5 (propynyl)uracil,5 (trifluoromethyl)uracil, 6 (azo)uracil, dihydrouracil, N3(methyl)uracil, 5-uracil (i.e., pseudouracil), 2 (thio)pseudouracil,4(thio)pseudouracil,2,4-(dithio)psuedouracil, 5-(alkyl)pseudouracil,5-(methyl)pseudouracil, 5-(alkyl)-2-(thio)pseudouracil,5-(methyl)-2-(thio)pseudouracil, 5-(alkyl)-4 (thio)pseudouracil,5-(methyl)-4 (thio)pseudouracil, 5-(alkyl)-2,4 (dithio)pseudouracil,5-(methyl)-2,4 (dithio)pseudouracil, 1 substituted pseudouracil, 1substituted 2(thio)-pseudouracil, 1 substituted 4 (thio)pseudouracil, 1substituted 2,4-(dithio)pseudouracil, 1(aminocarbonylethylenyl)-pseudouracil, 1(aminocarbonylethylenyl)-2(thio)-pseudouracil, 1(aminocarbonylethylenyl)-4 (thio)pseudouracil, 1(aminocarbonylethylenyl)-2,4-(dithio)pseudouracil, 1(aminoalkylaminocarbonylethylenyl)-pseudouracil, 1(aminoalkylamino-carbonylethylenyl)-2(thio)-pseudouracil, 1(aminoalkylaminocarbonylethylenyl)-4 (thio)pseudouracil, 1(aminoalkylaminocarbonylethylenyl)-2,4-(dithio)pseudouracil,1,3-(diaza)-2-(oxo)-phenoxazin-1-yl,1-(aza)-2-(thio)-3-(aza)-phenoxazin-1-yl,1,3-(diaza)-2-(oxo)-phenthiazin-1-yl,1-(aza)-2-(thio)-3-(aza)-phenthiazin-1-yl, 7-substituted1,3-(diaza)-2-(oxo)-phenoxazin-1-yl, 7-substituted1-(aza)-2-(thio)-3-(aza)-phenoxazin-1-yl, 7-substituted1,3-(diaza)-2-(oxo)-phenthiazin-1-yl, 7-substituted1-(aza)-2-(thio)-3-(aza)-phenthiazin-1-yl,7-(aminoalkylhydroxy)-1,3-(diaza)-2-(oxo)-phenoxazin-1-yl,7-(aminoalkylhydroxy)-1-(aza)-2-(thio)-3-(aza)-phenoxazin-1-yl,7-(aminoalkylhydroxy)-1,3-(diaza)-2-(oxo)-phenthiazin-1-yl,7-(aminoalkylhydroxy)-1-(aza)-2-(thio)-3-(aza)-phenthiazin-1-yl,7-(guanidiniumalkylhydroxy)-1,3-(diaza)-2-(oxo)-phenoxazin-1-yl,7-(guanidiniumalkylhydroxy)-1-(aza)-2-(thio)-3-(aza)-phenoxazin-1-yl,7-(guanidiniumalkylhydroxy)-1,3-(diaza)-2-(oxo)-phenthiazin-1-yl,7-(guanidiniumalkylhydroxy)-1-(aza)-2-(thio)-3-(aza)-phenthiazin-1-yl,1,3,5-(triaza)-2,6-(dioxa)-naphthalene, inosine, xanthine, hypoxanthine,nubularine, tubercidine, isoguanisine, inosinyl, 2-aza-inosinyl,7-deaza-inosinyl, nitroimidazolyl, nitropyrazolyl, nitrobenzimidazolyl,nitroindazolyl, aminoindolyl, pyrrolopyrimidinyl,3-(methyl)isocarbostyrilyl, 5-(methyl)isocarbostyrilyl,3-(methyl)-7-(propynyl)isocarbostyrilyl, 7-(aza)indolyl,6-(methyl)-7-(aza)indolyl, imidizopyridinyl,9-(methyl)-imidizopyridinyl, pyrrolopyrizinyl, isocarbostyrilyl,7-(propynyl)isocarbostyrilyl, propynyl-7-(aza)indolyl,2,4,5-(trimethyl)phenyl, 4-(methyl)indolyl, 4,6-(dimethyl)indolyl,phenyl, napthalenyl, anthracenyl, phenanthracenyl, pyrenyl, stilbenzyl,tetracenyl, pentacenyl, difluorotolyl,4-(fluoro)-6-(methyl)benzimidazole, 4-(methyl)benzimidazole,6-(azo)thymine, 2-pyridinone, 5 nitroindole, 3 nitropyrrole,6-(aza)pyrimidine, 2 (amino)purine, 2,6-(diamino)purine, 5 substitutedpyrimidines, N2-substituted purines, N6-substituted purines,06-substituted purines, substituted 1,2,4-triazoles,pyrrolo-pyrimidin-2-on-3-yl, 6-phenyl-pyrrolo-pyrimidin-2-on-3-yl,para-substituted-6-phenyl-pyrrolo-pyrimidin-2-on-3-yl,ortho-substituted-6-phenyl-pyrrolo-pyrimidin-2-on-3-yl,bis-ortho-substituted-6-phenyl-pyrrolo-pyrimidin-2-on-3-yl,para-(aminoalkylhydroxy)-6-phenyl-pyrrolo-pyrimidin-2-on-3-yl,ortho-(aminoalkylhydroxy)-6-phenyl-pyrrolo-pyrimidin-2-on-3-yl,bis-ortho-(aminoalkylhydroxy)-6-phenyl-pyrrolo-pyrimidin-2-on-3-yl,pyridopyrimidin-3-yl, 2-oxo-7-amino-pyridopyrimidin-3-yl,2-oxo-pyridopyrimidine-3-yl, or any O-alkylated or N-alkylatedderivatives thereof. Modified nucleosides also include natural basesthat comprise conjugated moieties, e.g. a ligand. As discussed hereinabove, the RNA containing the modified nucleosides must be translatablein a host cell (i.e., does not prevent translation of the polypeptideencoded by the modified RNA). For example, transcripts containing s2Uand m6A are translated poorly in rabbit reticulocyte lysates, whilepseudouridine, m5U, and m5C are compatible with efficient translation.In addition, it is known in the art that 2′-fluoro-modified bases usefulfor increasing nuclease resistance of a transcript, leads to veryinefficient translation. Translation can be assayed by one of ordinaryskill in the art using e.g., a rabbit reticulocyte lysate translationassay.

Further modified nucleobases include those disclosed in U.S. Pat. No.3,687,808, those disclosed in Modified Nucleosides in Biochemistry,Biotechnology and Medicine, Herdewijn, P. ed. Wiley-VCH, 2008; thosedisclosed in Int. Appl. No. PCT/US09/038,425, filed Mar. 26, 2009; thosedisclosed in The Concise Encyclopedia Of Polymer Science AndEngineering, pages 858-859, Kroschwitz, J. L, ed. John Wiley & Sons,1990, and those disclosed by Englisch et al., Angewandte Chemie,International Edition, 1991, 30, 613.

Representative U.S. patents that teach the preparation of certain of theabove noted modified nucleobases as well as other modified nucleobasesinclude, but are not limited to, the above noted U.S. Pat. No.3,687,808, as well as U.S. Pat. Nos. 4,845,205; 5,130,30; 5,134,066;5,175,273; 5,367,066; 5,432,272; 5,457,187; 5,457,191; 5,459,255;5,484,908; 5,502,177; 5,525,711; 5,552,540; 5,587,469; 5,594,121,5,596,091; 5,614,617; 5,681,941; 6,015,886; 6,147,200; 6,166,197;6,222,025; 6,235,887; 6,380,368; 6,528,640; 6,639,062; 6,617,438;7,045,610; 7,427,672; and 7,495,088, each of which is hereinincorporated by reference in its entirety, and U.S. Pat. No. 5,750,692,also herein incorporated by reference in its entirety.

Another modification for use with the synthetic, modified RNAs describedherein involves chemically linking to the RNA one or more ligands,moieties or conjugates that enhance the activity, cellular distributionor cellular uptake of the RNA. Ligands can be particularly useful where,for example, a synthetic, modified RNA is administered in vivo. Suchmoieties include but are not limited to lipid moieties such as acholesterol moiety (Letsinger et al., Proc. Natl. Acid. Sci. USA, 1989,86: 6553-6556, herein incorporated by reference in its entirety), cholicacid (Manoharan et al., Biorg. Med. Chem. Let., 1994, 4:1053-1060,herein incorporated by reference in its entirety), a thioether, e.g.,beryl-S-tritylthiol (Manoharan et al., Ann. N.Y. Acad. Sci., 1992,660:306-309; Manoharan et al., Biorg. Med. Chem. Let., 1993,3:2765-2770, each of which is herein incorporated by reference in itsentirety), a thiocholesterol (Oberhauser et al., Nucl. Acids Res., 1992,20:533-538, herein incorporated by reference in its entirety), analiphatic chain, e.g., dodecandiol or undecyl residues (Saison-Behmoaraset al., EMBO J, 1991, 10:1111-1118; Kabanov et al., FEBS Lett., 1990,259:327-330; Svinarchuk et al., Biochimie, 1993, 75:49-54, each of whichis herein incorporated by reference in its entirety), a phospholipid,e.g., di-hexadecyl-rac-glycerol or triethyl-ammonium1,2-di-O-hexadecyl-rac-glycero-3-phosphonate (Manoharan et al.,Tetrahedron Lett., 1995, 36:3651-3654; Shea et al., Nucl. Acids Res.,1990, 18:3777-3783, each of which is herein incorporated by reference inits entirety), a polyamine or a polyethylene glycol chain (Manoharan etal., Nucleosides & Nucleotides, 1995, 14:969-973, herein incorporated byreference in its entirety), or adamantane acetic acid (Manoharan et al.,Tetrahedron Lett., 1995, 36:3651-3654, herein incorporated by referencein its entirety), a palmityl moiety (Mishra et al., Biochim. Biophys.Acta, 1995, 1264:229-237, herein incorporated by reference in itsentirety), or an octadecylamine or hexylamino-carbonyloxycholesterolmoiety (Crooke et al., J. Pharmacol. Exp. Ther., 1996, 277:923-937,herein incorporated by reference in its entirety).

The synthetic, modified RNAs described herein can further comprise a 5′cap. In some embodiments of the aspects described herein, the synthetic,modified RNAs comprise a 5′ cap comprising a modified guanine nucleotidethat is linked to the 5′ end of an RNA molecule using a 5′-5′triphosphate linkage. As used herein, the term “5′ cap” is also intendedto encompass other 5′ cap analogs including, e.g., 5′ diguanosine cap,tetraphosphate cap analogs having a methylene-bis(phosphonate) moiety(see e.g., Rydzik, A M et al., (2009) Org Biomol Chem 7(22):4763-76),dinucleotide cap analogs having a phosphorothioate modification (seee.g., Kowalska, J. et al., (2008) RNA 14(6):1119-1131), cap analogshaving a sulfur substitution for a non-bridging oxygen (see e.g.,Grudzien-Nogalska, E. et al., (2007) RNA 13(10): 1745-1755),N7-benzylated dinucleoside tetraphosphate analogs (see e.g., Grudzien,E. et al., (2004) RNA 10(9):1479-1487), or anti-reverse cap analogs (seee.g., Jemielity, J. et al., (2003) RNA 9(9): 1108-1122 and Stepinski, J.et al., (2001) RNA 7(10):1486-1495). In one such embodiment, the 5′ capanalog is a 5′ diguanosine cap. In some embodiments, the synthetic,modified RNA does not comprise a 5′ triphosphate.

The 5′ cap is important for recognition and attachment of an mRNA to aribosome to initiate translation. The 5′ cap also protects thesynthetic, modified RNA from 5′ exonuclease mediated degradation. It isnot an absolute requirement that a synthetic, modified RNA comprise a 5′cap, and thus in other embodiments the synthetic, modified RNAs lack a5′ cap. However, due to the longer half-life of synthetic, modified RNAscomprising a 5′ cap and the increased efficiency of translation,synthetic, modified RNAs comprising a 5′ cap are preferred herein.

The synthetic, modified RNAs described herein can further comprise a 5′and/or 3′ untranslated region (UTR). Untranslated regions are regions ofthe RNA before the start codon (5′) and after the stop codon (3′), andare therefore not translated by the translation machinery. Modificationof an RNA molecule with one or more untranslated regions can improve thestability of an mRNA, since the untranslated regions can interfere withribonucleases and other proteins involved in RNA degradation. Inaddition, modification of an RNA with a 5′ and/or 3′ untranslated regioncan enhance translational efficiency by binding proteins that alterribosome binding to an mRNA. Modification of an RNA with a 3′ UTR can beused to maintain a cytoplasmic localization of the RNA, permittingtranslation to occur in the cytoplasm of the cell. In one embodiment,the synthetic, modified RNAs described herein do not comprise a 5′ or 3′UTR. In another embodiment, the synthetic, modified RNAs comprise eithera 5′ or 3′ UTR. In another embodiment, the synthetic, modified RNAsdescribed herein comprise both a 5′ and a 3′ UTR. In one embodiment, the5′ and/or 3′ UTR is selected from an mRNA known to have high stabilityin the cell (e.g., a murine alpha-globin 3′ UTR). In some embodiments,the 5′ UTR, the 3′ UTR, or both comprise one or more modifiednucleosides.

In some embodiments, the synthetic, modified RNAs described hereinfurther comprise a Kozak sequence. The “Kozak sequence” refers to asequence on eukaryotic mRNA having the consensus (gcc)gccRccAUGG SEQ IDNO: 1481, where R is a purine (adenine or guanine) three bases upstreamof the start codon (AUG), which is followed by another ‘G’. The Kozakconsensus sequence is recognized by the ribosome to initiate translationof a polypeptide. Typically, initiation occurs at the first AUG codonencountered by the translation machinery that is proximal to the 5′ endof the transcript. However, in some cases, this AUG codon can bebypassed in a process called leaky scanning. The presence of a Kozaksequence near the AUG codon will strengthen that codon as the initiatingsite of translation, such that translation of the correct polypeptideoccurs. Furthermore, addition of a Kozak sequence to a synthetic,modified RNA will promote more efficient translation, even if there isno ambiguity regarding the start codon. Thus, in some embodiments, thesynthetic, modified RNAs described herein further comprise a Kozakconsensus sequence at the desired site for initiation of translation toproduce the correct length polypeptide. In some such embodiments, theKozak sequence comprises one or more modified nucleosides.

In some embodiments, the synthetic, modified RNAs described hereinfurther comprise a “poly (A) tail”, which refers to a 3′ homopolymerictail of adenine nucleotides, which can vary in length (e.g., at least 5adenine nucleotides) and can be up to several hundred adeninenucleotides). The inclusion of a 3′ poly(A) tail can protect thesynthetic, modified RNA from degradation in the cell, and alsofacilitates extra-nuclear localization to enhance translationefficiency. In some embodiments, the poly(A) tail comprises between 1and 500 adenine nucleotides; in other embodiments the poly(A) tailcomprises at least 5, at least 10, at least 20, at least 30, at least40, at least 50, at least 60, at least 70, at least 80, at least 90, atleast 100, at least 110, at least 120, at least 130, at least 140, atleast 150, at least 160, at least 170, at least 180, at least 190, atleast 200, at least 225, at least 250, at least 275, at least 300, atleast 325, at least 350, at least 375, at least 400, at least 425, atleast 450, at least 475, at least 500 adenine nucleotides or more. Inone embodiment, the poly(A) tail comprises between 1 and 150 adeninenucleotides. In another embodiment, the poly(A) tail comprises between90 and 120 adenine nucleotides. In some such embodiments, the poly(A)tail comprises one or more modified nucleosides.

It is contemplated that one or more modifications to the synthetic,modified RNAs described herein permit greater stability of thesynthetic, modified RNA in a cell. To the extent that such modificationspermit translation and either reduce or do not exacerbate a cell'sinnate immune or interferon response to the synthetic, modified RNA withthe modification, such modifications are specifically contemplated foruse herein. Generally, the greater the stability of a synthetic,modified RNA, the more protein can be produced from that synthetic,modified RNA. Typically, the presence of AU-rich regions in mammalianmRNAs tend to destabilize transcripts, as cellular proteins arerecruited to AU-rich regions to stimulate removal of the poly(A) tail ofthe transcript. Loss of a poly(A) tail of a synthetic, modified RNA canresult in increased RNA degradation. Thus, in one embodiment, asynthetic, modified RNA as described herein does not comprise an AU-richregion. In particular, it is preferred that the 3′ UTR substantiallylacks AUUUA sequence elements.

In one embodiment, a ligand alters the cellular uptake, intracellulartargeting or half-life of a synthetic, modified RNA into which it isincorporated. In some embodiments a ligand provides an enhanced affinityfor a selected target, e.g., molecule, cell or cell type, intracellularcompartment, e.g., mitochondria, cytoplasm, peroxisome, lysosome, as,e.g., compared to a composition absent such a ligand. Preferred ligandsdo not interfere with expression of a polypeptide from the synthetic,modified RNA.

Ligands can include a naturally occurring substance, such as a protein(e.g., human serum albumin (HSA), low-density lipoprotein (LDL), orglobulin); carbohydrate (e.g., a dextran, pullulan, chitin, chitosan,inulin, cyclodextrin or hyaluronic acid); or a lipid. The ligand canalso be a recombinant or synthetic molecule, such as a syntheticpolymer, e.g., a synthetic polyamino acid. Examples of polyamino acidsinclude polylysine (PLL), poly L aspartic acid, poly L-glutamic acid,styrene-maleic acid anhydride copolymer, poly(L-lactide-co-glycolied)copolymer, divinyl ether-maleic anhydride copolymer,N-(2-hydroxypropyl)methacrylamide copolymer (HMPA), polyethylene glycol(PEG), polyvinyl alcohol (PVA), polyurethane, poly(2-ethylacryllicacid), N-isopropylacrylamide polymers, or polyphosphazine. Example ofpolyamines include: polyethylenimine, polylysine (PLL), spermine,spermidine, polyamine, pseudopeptide-polyamine, peptidomimeticpolyamine, dendrimer polyamine, arginine, amidine, protamine, cationiclipid, cationic porphyrin, quaternary salt of a polyamine, or an alphahelical peptide.

Ligands can also include targeting groups, e.g., a cell targeting agent,(e.g., a lectin, glycoprotein, lipid or protein), or an antibody, thatbinds to a specified cell type such as a fibroblast cell. A targetinggroup can be, for example, a thyrotropin, melanotropin, lectin,glycoprotein, surfactant protein A, Mucin carbohydrate, multivalentlactose, multivalent galactose, N-acetyl-galactosamine,N-acetyl-glucosamine multivalent mannose, multivalent fucose,glycosylated polyaminoacids, multivalent galactose, transferrin,bisphosphonate, polyglutamate, polyaspartate, a lipid, cholesterol, asteroid, bile acid, folate, vitamin B 12, biotin, or an RGD peptide orRGD peptide mimetic, among others.

Other examples of ligands include dyes, intercalating agents (e.g.acridines), cross-linkers (e.g. psoralene, mitomycin C), porphyrins(TPPC4, texaphyrin, Sapphyrin), polycyclic aromatic hydrocarbons (e.g.,phenazine, dihydrophenazine), artificial endonucleases (e.g. EDTA),lipophilic molecules, e.g., cholesterol, cholic acid, adamantane aceticacid, 1-pyrene butyric acid, dihydrotestosterone,1,3-Bis-O(hexadecyl)glycerol, geranyloxyhexyl group, hexadecylglycerol,borneol, menthol, 1,3-propanediol, heptadecyl group, palmitic acid,myristic acid,O3-(oleoyl)lithocholic acid, O3-(oleoyl)cholenic acid,dimethoxytrityl, or phenoxazine) and peptide conjugates (e.g.,antennapedia peptide, Tat peptide), alkylating agents, amino, mercapto,PEG (e.g., PEG-40K), MPEG, [MPEG]2, polyamino, alkyl, substituted alkyl,radiolabeled markers, enzymes, haptens (e.g. biotin), andtransport/absorption facilitators (e.g., aspirin, vitamin E, folicacid).

Ligands can be proteins, e.g., glycoproteins, or peptides, e.g.,molecules having a specific affinity for a co-ligand, or antibodiese.g., an antibody, that binds to a specified cell type such as afibroblast cell, or other cell useful in the production of polypeptides.Ligands can also include hormones and hormone receptors. They can alsoinclude non-peptidic species, such as lipids, lectins, carbohydrates,vitamins, cofactors, multivalent lactose, multivalent galactose,N-acetyl-galactosamine, N-acetyl-glucosamine multivalent mannose, ormultivalent fucose.

The ligand can be a substance, e.g., a drug, which can increase theuptake of the synthetic, modified RNA or a composition thereof into thecell, for example, by disrupting the cell's cytoskeleton, e.g., bydisrupting the cell's microtubules, microfilaments, and/or intermediatefilaments. The drug can be, for example, taxol, vincristine,vinblastine, cytochalasin, nocodazole, japlakinolide, latrunculin A,phalloidin, swinholide A, indanocine, or myoservin.

One exemplary ligand is a lipid or lipid-based molecule. A lipid orlipid-based ligand can (a) increase resistance to degradation, and/or(b) increase targeting or transport into a target cell or cell membrane.A lipid based ligand can be used to modulate, e.g., binding of themodified RNA composition to a target cell.

In another aspect, the ligand is a moiety, e.g., a vitamin, which istaken up by a host cell. Exemplary vitamins include vitamin A, E, and K.Other exemplary vitamins include B vitamin, e.g., folic acid, B 12,riboflavin, biotin, pyridoxal or other vitamins or nutrients taken up,for example, by cancer cells. Also included are HSA and low densitylipoprotein (LDL).

In another aspect, the ligand is a cell-permeation agent, preferably ahelical cell-permeation agent. Preferably, the agent is amphipathic. Anexemplary agent is a peptide such as tat or antennopedia. If the agentis a peptide, it can be modified, including a peptidylmimetic,invertomers, non-peptide or pseudo-peptide linkages, and use of D-aminoacids. The helical agent is preferably an alpha-helical agent, whichpreferably has a lipophilic and a lipophobic phase.

A “cell permeation peptide” is capable of permeating a cell, e.g., amicrobial cell, such as a bacterial or fungal cell, or a mammalian cell,such as a human cell. A microbial cell-permeating peptide can be, forexample, an α-helical linear peptide (e.g., LL-37 or Ceropin P1), adisulfide bond-containing peptide (e.g., α-defensin, β-defensin orbactenecin), or a peptide containing only one or two dominating aminoacids (e.g., PR-39 or indolicidin). For example, a cell permeationpeptide can be a bipartite amphipathic peptide, such as MPG, which isderived from the fusion peptide domain of HIV-1 gp41 and the NLS of SV40large T antigen (Simeoni et al., Nucl. Acids Res. 31:2717-2724, 2003).

The synthetic, modified RNAs described herein can be synthesized and/ormodified by methods well established in the art, such as those describedin “Current Protocols in Nucleic Acid Chemistry,” Beaucage, S. L. et al.(Edrs.), John Wiley & Sons, Inc., New York, N.Y., USA, which is herebyincorporated herein by reference in its entirety. Transcription methodsare described further herein in the Examples.

In one embodiment of the aspects described herein, a template for asynthetic, modified RNA is synthesized using “splint-mediated ligation,”which allows for the rapid synthesis of DNA constructs by controlledconcatenation of long oligos and/or dsDNA PCR products and without theneed to introduce restriction sites at the joining regions. It can beused to add generic untranslated regions (UTRs) to the coding sequencesof genes during T7 template generation. Splint mediated ligation canalso be used to add nuclear localization sequences to an open readingframe, and to make dominant-negative constructs with point mutationsstarting from a wild-type open reading frame. Briefly, single-strandedand/or denatured dsDNA components are annealed to splint oligos whichbring the desired ends into conjunction, the ends are ligated by athermostable DNA ligase and the desired constructs amplified by PCR. Asynthetic, modified RNA is then synthesized from the template using anRNA polymerase in vitro. After synthesis of a synthetic, modified RNA iscomplete, the DNA template is removed from the transcription reactionprior to use with the methods described herein.

In some embodiments of these aspects, the synthetic, modified RNAs arefurther treated with an alkaline phosphatase.

One skilled in the art readily appreciates that the present invention iswell adapted to carry out the objects and obtain the ends and advantagesmentioned, as well as those inherent therein. The details of thedescription and the examples herein are representative of certainembodiments, are exemplary, and are not intended as limitations on thescope of the invention. Modifications therein and other uses will occurto those skilled in the art. These modifications are encompassed withinthe spirit of the invention. It will be readily apparent to a personskilled in the art that varying substitutions and modifications may bemade to the invention disclosed herein without departing from the scopeand spirit of the invention.

The articles “a” and “an” as used herein in the specification and in theclaims, unless clearly indicated to the contrary, should be understoodto include the plural referents. Claims or descriptions that include“or” between one or more members of a group are considered satisfied ifone, more than one, or all of the group members are present in, employedin, or otherwise relevant to a given product or process unless indicatedto the contrary or otherwise evident from the context. The inventionincludes embodiments in which exactly one member of the group is presentin, employed in, or otherwise relevant to a given product or process.The invention also includes embodiments in which more than one, or allof the group members are present in, employed in, or otherwise relevantto a given product or process. Furthermore, it is to be understood thatthe invention provides all variations, combinations, and permutations inwhich one or more limitations, elements, clauses, descriptive terms,etc., from one or more of the listed claims is introduced into anotherclaim dependent on the same base claim (or, as relevant, any otherclaim) unless otherwise indicated or unless it would be evident to oneof ordinary skill in the art that a contradiction or inconsistency wouldarise. It is contemplated that all embodiments described herein areapplicable to all different aspects of the invention where appropriate.It is also contemplated that any of the embodiments or aspects can befreely combined with one or more other such embodiments or aspectswhenever appropriate. Where elements are presented as lists, e.g., inMarkush group or similar format, it is to be understood that eachsubgroup of the elements is also disclosed, and any element(s) can beremoved from the group. It should be understood that, in general, wherethe invention, or aspects of the invention, is/are referred to ascomprising particular elements, features, etc., certain embodiments ofthe invention or aspects of the invention consist, or consistessentially of, such elements, features, etc. For purposes of simplicitythose embodiments have not in every case been specifically set forth inso many words herein. It should also be understood that any embodimentor aspect of the invention can be explicitly excluded from the claims,regardless of whether the specific exclusion is recited in thespecification. For example, any one or more active agents, additives,ingredients, optional agents, types of organism, disorders, subjects, orcombinations thereof, can be excluded.

Where the claims or description relate to a composition of matter, it isto be understood that methods of making or using the composition ofmatter according to any of the methods disclosed herein, and methods ofusing the composition of matter for any of the purposes disclosed hereinare aspects of the invention, unless otherwise indicated or unless itwould be evident to one of ordinary skill in the art that acontradiction or inconsistency would arise. Where the claims ordescription relate to a method, e.g., it is to be understood thatmethods of making compositions useful for performing the method, andproducts produced according to the method, are aspects of the invention,unless otherwise indicated or unless it would be evident to one ofordinary skill in the art that a contradiction or inconsistency wouldarise.

Where ranges are given herein, the invention includes embodiments inwhich the endpoints are included, embodiments in which both endpointsare excluded, and embodiments in which one endpoint is included and theother is excluded. It should be assumed that both endpoints are includedunless indicated otherwise. Furthermore, it is to be understood thatunless otherwise indicated or otherwise evident from the context andunderstanding of one of ordinary skill in the art, values that areexpressed as ranges can assume any specific value or subrange within thestated ranges in different embodiments of the invention, to the tenth ofthe unit of the lower limit of the range, unless the context clearlydictates otherwise. It is also understood that where a series ofnumerical values is stated herein, the invention includes embodimentsthat relate analogously to any intervening value or range defined by anytwo values in the series, and that the lowest value may be taken as aminimum and the greatest value may be taken as a maximum. Numericalvalues, as used herein, include values expressed as percentages. For anyembodiment of the invention in which a numerical value is prefaced by“about” or “approximately”, the invention includes an embodiment inwhich the exact value is recited. For any embodiment of the invention inwhich a numerical value is not prefaced by “about” or “approximately”,the invention includes an embodiment in which the value is prefaced by“about” or “approximately”.

Approximately” or “about” generally includes numbers that fall within arange of 1% or in some embodiments within a range of 5% of a number orin some embodiments within a range of 10% of a number in eitherdirection (greater than or less than the number) unless otherwise statedor otherwise evident from the context (except where such number wouldimpermissibly exceed 100% of a possible value). It should be understoodthat, unless clearly indicated to the contrary, in any methods claimedherein that include more than one act, the order of the acts of themethod is not necessarily limited to the order in which the acts of themethod are recited, but the invention includes embodiments in which theorder is so limited. It should also be understood that unless otherwiseindicated or evident from the context, any product or compositiondescribed herein may be considered “isolated”.

As used herein the term “comprising” or “comprises” is used in referenceto compositions, methods, and respective component(s) thereof, that areessential to the invention, yet open to the inclusion of unspecifiedelements, whether essential or not.

As used herein the term “consisting essentially of” refers to thoseelements required for a given embodiment. The term permits the presenceof additional elements that do not materially affect the basic and novelor functional characteristic(s) of that embodiment of the invention.

The term “consisting of” refers to compositions, methods, and respectivecomponents thereof as described herein, which are exclusive of anyelement not recited in that description of the embodiment.

EXAMPLES Example 1

Transcription activator-like effector nucleases (TALENs) bind as a pairaround a genomic site, in which a double-strand break (DSB) isintroduced by a dimer of FokI nuclease domains. The use of a TALENgenome-editing system to rapidly and efficiently generate mutant allelesof 15 different genes in human pluripotent stem cells (hPSCs) as a meansof performing rigorous disease modeling was recently reported (Ding etal., Cell Stem Cell 12:238-251 (2013)); the proportions of clonesbearing at least one mutant allele ranged from 2%-34%.

As described below, the relative efficacies of CRISPRs and TALENstargeting the same genomic sites in the same hPSC lines was assessedwith the use of the same delivery platform described previously (Ding etal., Cell Stem Cell 12:238-251 (2013)). In the TALEN genome-editingsystem, the CAG promoter was used to co-translate (via a viral 2Apeptide) each TALEN with green fluorescent protein (GFP) or redfluorescent protein (RFP). For CRISPRs, a human codon-optimized Cas9gene was subcloned with a C-terminal nuclear localization signal (Maliet al., Science 339:823-826 (2013)) into the same CAG expression plasmidwith GFP, and the guide RNA (gRNA) was separately expressed from aplasmid with the human U6 polymerase III promoter (Mali et al., Science339:823-826 (2013)). The 20-nucleotide protospacer sequence for eachgRNA was introduced using polymerase chain reaction (PCR)-based methods.Whether using TALENs or CRISPRs, equal amounts of the two plasmids wereco-electroporated into hPSCs (either 25 μg of each plasmid, or 12.5 μgof each plasmid along with 25 μg of a DNA repair template if attemptingknock-in) followed by fluorescence-activated cell sorting (FACS) after24-48 hours, clonal expansion of single cells, and screening formutations at the genomic target site via PCR.

gRNAs were designed matching G(N)19NGG sequences in seven loci in sixgenes (AKT2, CELSR2, CIITA, GLUT4, LINC00116, and SORT1) previouslysuccessfully targeted with TALENs (Ding et al., Cell Stem Cell12:238-251 (2013)) and one additional locus in LDLR. In this system,CRISPRs consistently and substantially outperformed TALENs across lociand hPSC lines (see Table S1). The TALENs yielded clones with at leastone mutant allele at efficiencies of 0%-34%, but matched CRISPRs yieldedmutant clones at efficiencies of 51%-79% (Table S1). Just as withTALENs, CRISPRs produced a variety of indels of sizes ranging from onenucleotide to several dozen nucleotides in size, centered on thepredicted cleavage sites, suggesting that non-homologous end-joiningmutagenesis occurs in the same way regardless of whether CRISPRs orTALENs are used. Moreover, CRISPRs readily generated homozygous mutantclones (7%-25% of all clones; Table S1) as discerned by sequencing.

Knock-in of E17K mutations into AKT2 was also attempted using a67-nucleotide single-stranded DNA oligonucleotide as previouslydescribed (Ding et al., Cell Stem Cell 12:238-251 (2013)). Although thepredicted CRISPR cleavage site lay 11 and 13 nucleotides from the pointmutations, respectively, the CRISPR yielded knock-in clones at a rate of11%, whereas TALENs yielded only 1.6% (Table S1).

TABLE S1Targeting Efficiency of CRISPRs Versus TALENs in Human Pluripotent Stem CellsCRISPRs Effi- Chromosome: TALENs ciency Position Efficiency of (Start of(Mutants/ Efficiency Homo- Target Cell Clones (Mutants/Clones zygousGene Sequence) Target Sequence^(a) Line^(b) Screened)^(c) Screened)^(c)Mutants AKT2 chr19:40762982 TCCCTTCCTGCCTCATTTCAGGTGAATACA HUES 9  8.9%(SEQ ID NO: 335) TCAAGACCTGGAGGCCA (17/192) AKT2 chr19:40762982TCCCTTCCT GCC|TCATTTCAGGTGAATAC HUES 9 (SEQ ID NO: 60.6% (86/142) 12.7%ATCAAGACCTGGAGGCCA 336) (18/142) CELSR2 chr1:109817568TGCTGGCTCGGCTGCCCTGAGGTTGCTCAA HUES 1  3.5% (SEQ ID NO: 337)TCAAGCACAGGTTTCAA (18/506) CELSR2 chr1:109817568TGCTGGCTCGGCTGCCCTGAGGTTGCTCAA HUES 1 (SEQ ID NO: 66.2% (45/68)  7.4%TCAAG|CAC AGGTTTCAA 338) (5/68) CIITA chr16:10989200TAACAGCGATGCTGACCCCCTGTGCCTCTA BJ-RiPS 12.7% (SEQ ID NO: 339)CCACTTCTATGACCAGA (37/292) CIITA chr16:10989206CGATGCTGACCCCCTGTGCCTCTACCA BJ-RiPS (SEQ ID NO: 78.7% (96/122) 11.5%CTT|CTATGACCAGATGGACC 340) (14/122) GLUT4 chr17:7186601TGGTCCTTGCTGTGTTCTCTGCGGTGCTTG HUES 9 33.5% (SEQ ID NO: 341)GCTCCCTGCAGTTTGGGTA (52/155) GLUT4 chr17:7186601TGGTCCTTGCTGTGTTCT|CTGCGGTGCTT HUES 9 (SEQ ID NO: 66.5% (123/185) 24.9%GGCTCCCTGCAGTTTGGGTA 342) (46/185) LDLR chr19:11210899TGGGCGACAGATGCGAAAGAAACGAGTTC HUES 9    0% (SEQ ID NO: 343)CAGTGCCAAGACGGGAAA (0/568) LDLR chr19:11210917GAAACGAGTTCCAGTGCCAAGACGGGAAAT HUES 9 (SEQ ID NO: 51.1% (90/176)  8.0%GCATCTCCTAC|AAG TGG 344) (14/176) LINC00116 ch2:110970090TCAGAGAGGACACTGCAGTTGTCCGTGCTT HUES 9 29.5% (SEQ ID NO: 345)AGTAGCCTTCGCTTCTGGA (26/88) LINC00116 ch2:110970090TCAGAGAGGACATGCAGTTGTCCGTGCTAG HUES 9 (SEQ ID NO: 57.4% (93/162)  8.6%TAGCCTTCGC|TTCTGGA 346) (14/162) SORT1 chr1:109912203TGATGATCTCAGAGGCTCAGTATCCTTGTC HUES 1 22.2% (SEQ ID NO: 347) exon 2CTGGGTTGGAGATAGCA (128/576) SORT1 chr1:109912203TGATGATCTCAGAGGCTCAGTATCCTTG| HUES 1 (SEQ ID NO: 68.5% (100/146) 13.0%exon 2 TCC TGGGTTGGAGATAGCA 348) (19/146) SORT1 chr1:109910069TGGTAATTATGACTTTTGGACAGTCCAAGC HUES 9 10.9% (SEQ ID NO: 349) exon 3TATATCGAAGGTGAGATCA (21/192) SORT1 chr1:109910069TGGTAATTATGACTTTTGGACAGTCCAAG HUES 9 (SEQ ID NO: 75.9% (148/195) 10.3%exon 3 CTATAT|CGAAGGTGAGATCA 350) (20/195) AKT2 E17K chr19:40762982TCCCTTCCTGCCTCATTTCAGGTGA

TA HUES 9  1.6% (SEQ ID NO: 351) CATCAAGACCTGGAGGCCA (3/192)^(d)AKT2 E17K chr19:40762982 TCCCT

ATC HUES 9 (SEQ ID NO: 10.6% (10/94)^(d)  1.1% AAGACCTGGAGGCCA 352)(1/94)^(d) AKT2 chr5:22683972 CTATGCCCT

HUES 9 (SEQ ID NO: 0% (0/142)    0% off-target GAAATCCCTGGAGCTTGG 363)(0/142) ^(a)For TALENs, the binding sites are indicated with underlines,with the cleavage site predicted to be midway between the binding sites;for CRISPRs, the protospacer is underlined, the NGG motif is in bold(may be on the antisense strand), and the predicted cleavage site isindicated with “|”, for the AKT2 E17K target sequence, the sites of theknock-in mutations are indicated in bold/italics; for the AKT2off-target site, the two mismatches in the protospacer are indicated inbold/italics ^(b)HUES 1 and HUES 9 are human embryonic stem cell lines;BJ-RiPS is an induced pluripotent stem cell line ^(c)Mutants includesingle heterozygotes, compound heterozygotes, and homozygous mutants;TALEN data is from Table 1 of Ding et al. (2013),with the exception ofLDLR ^(d)Successfully inserted E17K knock-in mutations into an AKT2allele(s) using single-stranded DNA oligonucleotide (refer to FIG. 3 ofDing et al., 2013)

It is worth noting that the requirement for a G(N)19NGG target sequencesomewhat limits site selection. Because either DNA strand can betargeted, a target sequence occurs on average every 32 basepairs. Thisis no barrier for gene knockout, where any coding sequence can betargeted, but it may present difficulties when trying to knock in orcorrect a mutation at a specific location. However, the requirement fora G at the start of the protospacer is dictated by the use of the U6promoter to express the gRNA, and alternative CRISPR/Cas systems canrelieve this requirement (Cong et al., Science 339:819-823 (2013)). Thisallows for the use of (N)20NGG target sequences, which are found onaverage every 8 basepairs.

In addition, the extent of CRISPR off-target effects remains to bedefined and is highly sequence-dependent. Previous analyses havesuggested that one-nucleotide mismatches in the first half of theprotospacer are better tolerated than mismatches in second half (Jineket al., Science 337:816-821 (2012); Cong et al., Science 339:819-823(2013)). For the AKT2 sequence, there is a two-mismatch sequencediffering at nucleotides 1 and 3, in the more “tolerant” half of theprotospacer. Zero clones were obtained with mutations at this potentialoff-target site, as compared to 61% at the on-target site (Table S1).For one of the SORT1 sequences, use of a different human pluripotentstem cell line in which a single nucleotide polymorphism results in aone-nucleotide mismatch at the target site yielded mutant clones at anefficiency of 42%, compared to 66% in the original cell line. Thus,judicious selection of target sites is necessary to minimize systematicoff-target effects; target sites with perfect-match orsingle-nucleotide-mismatch sequences elsewhere in the genome should beavoided.

From a practical standpoint, CRISPRs are easier to implement thanTALENs. Each TALEN pair must be constructed de novo, whereas for CRISPRsthe Cas9 component is fixed and the gRNA requires only swapping of the20-nucleotide protospacer. Given this consideration and thedemonstration herein of substantially increased efficiency as a resultof replacing TALENs with CRISPRs in an otherwise identical system,CRISPRs appear to be a very powerful and broadly applicable tool forgenome editing, particularly in a therapeutic context.

Example 2: Modified Cas9 mRNA Functions to Efficiently IntroduceOn-Target Mutations

The inventors generated Figment (Fgm) knockout mice by CRIPSR/Cas9 geneediting utilizing a modified Cas9 mRNA. Fgm is a coding gene within thelong non-coding RNA Lnc-Rap-5 (referred to herein as Fgm (Lnc-Rap-5; seeSun et al., “Long noncoding RNAs regulate adipogenesis,” PNAS; 2013;110(9):3387-3392, incorporated herein by reference in its entirety). Theguide RNA (gRNA) sequence employed in this example was: 5′gaggcgaaagccactagcac 3′. The modified Cas9 mRNA used in this example wasmade using an in vitro transcription reaction in which pseudouridine and5-methyl-cytosine were reacted with unmodified nucleotides and randomlyintegrated into the resulting modified Cas9 mRNA. An exemplary protocolfor generating Fgm knockout mice using CRISPR/Cas9 gene editingutilizing a modified Cas9mRNA is shown in FIG. 19A. As shown in FIG.19A, 100 ng/l of the resulting modified Cas9 mRNA and 50 ng/l of theguide RNA noted above targeting Fgm (Lnc-Rap-5) were injected into 250C57BL/6 mouse zygotes that were subsequently transferred topseudo-pregnant mice and after weening screened for mutations by PCR. Asshown in the gel pictured in FIG. 19B, PCR screening revealed 63 mutantanimals out of 65. These results indicate that modified Cas9 mRNAfunctions in vivo to efficiently (i.e., 97% efficiency) introduce ontarget mutations in mammals.

Example 3: Mutational Analysis of Genome Edited HematopoieticStem-Progenitor Cells (HSPCs) by Target Capture Deep Sequencing

CRISPR/Cas9 has previously been shown to generate off-target mutationsto varying degrees depending upon experimental setting and cell type(Cho et al., 2014; Cradick et al., 2013; Fu et al., 2013; Fu et al.,2014; Hruscha et al., 2013; Lin et al., 2014). To examine this inprimary CD34⁺ HSPCs we performed target capture sequencing, of CD34⁺HSPCs-mPB subjected to CRISPR/Cas9 CCR5-editing. Experimental designincluded capture of each gRNA target site (n=6) and predicted off-targetsites (n=172) with expanded capture intervals of 500 base pairs flankingeach site to ensure accurate detection of any genetic lesion occurringat or near the selected sites (FIGS. 17A and 20). We have previouslyshown that this approach can also capture structural variationbreakpoints, such as translocations and inversions, in proximity to thecapture site (Talkowski et al., 2011) (See supplemental text and methodsfor detailed description). Sorted CD34⁺ HSPCs treated with Cas9 alone orin combination with multiple single gRNA (crCCR5_A, crCCR5_B, orcrCCR5_C) or dual gRNA combinations (crCCR5_A+B, crCCR5_C+D, orcrCCR5_D+Q) were sequenced to a mean target coverage of 3,390× acrosseach 23 bp gRNA sequence and PAM (range 379.6×-7,969.5×)(FIG. 17B).Analysis of the resulting data revealed highly efficacious on-targetmutagenesis with a diverse array of mutated sequence variants observedin both single-gRNA and dual-gRNA treatments (FIG. 17C). As expected wedetected small InDels of up to 10 bp in addition to varying singlenucleotide substitutions at the predicted target sites in thesingle-gRNA libraries. Strikingly, in each dual-gRNA library, no fewerthan 15 alternate mutant alleles were observed at either one of the gRNAsites (FIGS. 21-23). Notably, the extreme sequencing depth of ouranalysis permitted estimation of mutation frequency for each particularvariant, including mutations that were observed in only a few hundredthsof a percent of the sample sequenced (FIG. 24). Predicted deletions(i.e. deletions spanning between the two gRNA target sites) were themost common mutations observed (crCCR5_A+B: 19.95%; crCCR5_C+D: 20.45%;crCCR5_D+Q: 42.13%), while small InDels (crCCR5_A+B: 3.06%; crCCR5_C+D:0.50%; crCCR5_D+Q: 2.95%) were also frequent (FIG. 17C). Interestingly,for two dual gRNA combinations (crCCR5_A+B and crCCR5_D+Q) we alsoobserved inversions between the two predicted Cas9 cleavage sites(crCCR5_A+B: 3.06%; crCCR5_D+Q: 2.48%). The most efficacious dual gRNAcombination crCCR5_D+Q led to mutations in approximately 48% of thecaptured sequence reads (FIG. 17C).

We next examined the capture sequence reads at predicted off-targetsites in the genome (FIG. 20). An N-fold enrichment analysis wasperformed, wherein we compared the total number of non-referencesequencing reads at each predicted off-target site in gRNA treated andcontrol (Cas9 only) samples. This analysis generated a ratio where 1.0indicates an equivalent number of non-reference sequence reads in bothtreated and control samples, values less than 1.0 indicate fewernon-reference reads in treated samples, and values greater than 1.0indicate a greater number of non-reference reads in treated samples (seesupplementary materials for additional details) (FIG. 17D). Strikingly,this analysis showed that the mean enrichment of mutations at off-targetsites in all the gRNA-treated samples compared to control closelyconformed to the null hypothesis (i.e., 0.99-fold enrichment compared tocontrols) indicating that off-target mutation events were extremelyrare. Indeed, statistical evaluation of all captured off-target sitesyielded a single site (1/172; 0.6%) in the sample treated with gRNAcrCCR5_B alone that passed multiple test correction for a statisticallysignificant enrichment for off-target InDels in the gRNA crCCR5_Btreated libraries versus control (p≤7.6×10⁻¹¹) (FIGS. 24-25). When wescrutinized the sequencing reads from the only statistically significantoff-target site, which was located in the highly homologous CCR2 gene(FIG. 18A), we found that all sequence variants (36 out of 5,963 totalreads) were one or two base InDels, (FIG. 18B). Of note, the othersample in which gRNA crCCR5_B was used (in combination with gRNAcrCCR5_A) only 13 out of 5,339 reads supported mutation, however theseevents did not meet statistical significance above control or samplestreated with other gRNAs (FIG. 18B, FIG. 24). Thus, off-targetmutagenesis was exceedingly rare and moreover, the use of two gRNAs incombination did not increase the very low incidence of off-targetmutagenesis. We also performed targeted analyses for structuralvariation at all sites and though we could easily detect on-targetinversions in dual gRNA combination crCCR5_A+B and crCCR5_D+Q, there wasno evidence for inversion or translocation at any off-target sites inany of the treatments. These data indicate that on-target mutagenesisefficiency was very high, and further that off-target mutagenesis wasextremely infrequent for both single- and dual gRNA treatments.

Discussion

Our mutational analysis revealed highly efficacious mutagenesis ofon-target sites in CD34⁺ HSPCs. Single gRNAs generated a range ofmutations with the vast majority comprised of small InDels. In contrast,dual gRNA combinations largely led to predicted deletions through adiverse array of mutations including InDels and even inversions weredetected. Importantly, we only identified one statistically significantoff-target site in the highly homologous CCR2 gene, which occurred inone out of 6 experimental settings (gRNA crCCR5_B alone). Sequenceanalysis of gRNA crCCR5_B in comparison to the identified off-targetsite in CCR2 indicated that it perfectly matched in the seed region andcontained 3 sequence mismatches at the 5′ end of the gRNA sequence(positions 1, 4 and 6). This data is consistent with previous studiesshowing that mismatches in the 5′ proximal end of the gRNA are welltolerated by Cas9 (Lin et al., 2014; Wu et al., 2014). Our datatherefore supports the idea that judicious guide design is critical forminimizing off-target mutations. Of note, our very deep sequencinganalysis enabled detection of the sole off-target event we describe,whereas sequence analysis performed at lower sequencing depth—such as50× coverage that has been used in previous off-target analyses (Smithet al., 2014; Suzuki et al., 2014; Veres et al., 2014)—would have beenunable to detect this event. Overall, our analysis of CRISPR/Cas9mutational activity in CD34⁺ HSPCs revealed very high on-target mutationrates and extremely low incidence of off-target mutagenesis.

Off-Target Prediction and Capture Sequencing

Degenerate gRNA off-target sequences were predicted for each gRNAtargeting CCR5 using the CRISPR Design off-target prediction tool (Hsuet al., 2013). Off-target sequences were further supplemented byalignment of each gRNA to the human genome using BOWTIE of which allresults up to and including 3 mismatches were added to the totaloff-target list (Langmead et al., 2009). All instances of each predictedoff-target sequence existent in the human genome reference buildGRCh37v71 were recorded (FIG. 20). Each guide RNA target site (n=6) andpredicted off-target site (n=172) was selected for capture sequencingusing the Agilent SureSelectXT Target Enrichment System. Captureintervals were expanded by approximately 500 bp in both the 5′ and 3′directions to ensure exhaustive capture of the targeted region anddetection of any genetic lesion occurring at or near a predicted gRNAon- or off-target site, as we have previously shown accurate capabilityto detect translocations and inversions using targeted capture of probesin proximity to a rearrangement breakpoint using a CapBP procedure asdescribed (Talkowski et al., 2011). Probes were tiled with 60-foldgreater density over each predicted 23 bp on- or off-target gRNA bindingsite than the flanking kilobase of sequence. Isogenic CD34⁺ HSPCs-mPBwere transfected with CRISPR/Cas9 plasmids (one Cas9 only-treatedcontrol group, three treatment groups transfected with a single gRNA,and three treatment groups transfected with dual gRNAs). Sorted CD34⁺genome edited HSPCs were cultured for two weeks prior to DNA isolation.Capture libraries were prepared from DNA extracted from seven treatmentgroups. Capture libraries were sequenced as 101 bp paired-end reads onan Illumina HiSeq2000 platform.

NGS Data Processing and Computational Analysis

Read pairs were aligned to GRCh37v71 with Bwa-MEM v0.7.10-r789 (Li,arXiv 2013). Alignments were processed using PicardTools and SAMBLASTER(Faust and Hall, 2014). The Genome Analysis Toolkit (GATK)v3.1-1-g07a4bf8 was applied for base quality score recalibration,insertion/deletion (InDel) realignment, duplicate removal, and singlenucleotide variant (SNV) and InDel discovery and genotyping perpublished best-practice protocols (McKenna et al, Genome Res 2010;DePristo et al, Nat Genet 2011; Van der Auwera et al, 2013). SNVs andInDels were annotated using ANNOVAR (Wang et al., 2010). Structuralvariants (SVs) were detected with LUMPY v0.2.5 considering bothanomalous pair and split read evidence at a minimum call weightthreshold of 7 and an evidence set score ≤0.05 (Layer et al., 2014).Candidate copy number variants (CNVs) were further statisticallyassessed by Student's t-test for a concomitant change in depth ofcoverage across the putative CNV. As a final exhaustive measure, eachon- and off-target site was manually scrutinized in each capture libraryfor evidence supporting predictable mutagenesis that is not detectableby the computational algorithms due to low levels of mosaicism in thesequenced population.

Evaluation of Off-Target Mutation Frequency

A statistical framework was developed to assess off-target mutationalburden for each gRNA. For each off-target site (n=172), all reads withat least one nucleotide of overlap with that 23 bp off-target site werecollected and their CIGAR information was tabulated into categories asfollows: reads representing small InDels (CIGAR contains at least one“I” or “D”), reads potentially representative of other rearrangements(CIGAR contains at least one “S” or “H”), and reads reflecting referencesequence (CIGAR did not match either of the two former categories). Suchcounts were gathered at all 172 sites in all seven libraries and werefurther pooled to form comparison groups of “treatment” libraries(transfected gRNA matches corresponding off-target site gRNA) and“control” libraries (transfected gRNA does not match correspondingoff-target site gRNA). Next, at each off-target site, relative n-foldenrichment of each read classification between treatment and controllibraries was evaluated. Finally, a one-tailed Fisher's Exact Test wasperformed to assess the statistical significance of enrichment ofvariant reads in treatments versus controls at each off-target site,followed by Bonferroni correction to retain an experiment-widesignificance threshold of α=0.05.

REFERENCES

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1.-12. (canceled)
 13. A method for altering a target betathalassemia-associated polynucleotide sequence in a cell comprisingcontacting the beta thalassemia-associated polynucleotide sequence witha clustered regularly interspaced short palindromic repeats-associated(Cas) protein and from one to two ribonucleic acids, wherein theribonucleic acids direct Cas protein to and hybridize to a target motifof the target beta thalassemia-associated polynucleotide sequence,wherein the target beta thalassemia-associated polynucleotide sequenceis cleaved, and wherein the efficiency of alteration is from about 50%to about 80%. 14.-18. (canceled)
 19. The method according to claim 13,wherein the Cas protein is Streptococcus pyogenes Cas9 protein or afunctional portion thereof selected from the group consisting of a DNAbinding domain, at least one RNA binding domain, a helicase domain, andan endonuclease domain. 20.-21. (canceled)
 22. The method according toclaim 13, wherein the Cas protein is Cas9 protein from any bacterialspecies or functional portion thereof selected from the group consistingof a DNA binding domain, at least one RNA binding domain, a helicasedomain, and an endonuclease domain. 23.-24. (canceled)
 25. The methodaccording to claim 13, wherein the Cas protein is complexed with the oneto two ribonucleic acids. 26.-32. (canceled)
 33. The method according toclaim 13, wherein the target motif is G(N)19NGG. 34.-41. (canceled) 42.The method according to claim 13, wherein the alteration results inreduced expression of the target polynucleotide sequence, a knock out ofthe target polynucleotide sequence, or correction of the targetpolynucleotide sequence from an undesired sequence to a desiredsequence. 43.-57. (canceled)
 58. The method according to claim 13,wherein the cell is selected from the group consisting of a peripheralblood cell, a stem cell, a pluripotent cell, a hematopoietic stem cell,a CD34+ cell, a CD34+ mobilized peripheral blood cell, a CD34+ cordblood cell, a CD34+ bone marrow cell, a CD34⁺CD38-Lineage-CD90⁺CD45RA⁻cell, a primary human cell, a non-transformed human cell, andcombinations thereof. 59.-107. (canceled)
 108. The method according toclaim 13, wherein the target polynucleotide sequence is HBB.
 109. Themethod according to claim 108, wherein at least one of the one to tworibonucleic acids comprises a sequence selected from the groupconsisting of SEQ ID NOS. 814-908, or at least a 12 nucleotide fragmentthereof.
 110. The method according to claim 108, wherein at least one ofthe one to two ribonucleic acids comprises a sequence with a singlenucleotide mismatch to a sequence selected from the group consisting ofSEQ ID NOS. 814-908, or at least a 12 nucleotide fragment thereof.111.-173. (canceled)
 174. The method according to claim 13, wherein theone to two ribonucleic acids hybridize to a target motif that containsat least one mismatch when compared with all other genomic nucleotidesequences in the cell. 175.-193. (canceled)
 194. The method according toclaim 13, wherein at least one of the ribonucleic acids is a modifiedribonucleic acid comprising one to two modified nucleotides selectedfrom the group consisting of pseudouridine, 5-methylcytodine,2-thio-uridine, 5-methyluridine-5′-triphosphate,4-thiouridine-5′-triphosphate, 5,6-dihydrouridine-5′-triphosphate, and5-azauridine-5′-triphosphate. 195.-272. (canceled)
 273. The methodaccording to claim 13, wherein the cell was selected for Cas proteinexpression.
 274. The method according to claim 13, wherein the targetmotif of the target beta thalassemia-associated polynucleotide sequencecomprises nucleotides located between position 5246806 and position5248263 of human chromosome 11.